tag:blogger.com,1999:blog-3060898714439566244.post2516945567587550840..comments2023-09-24T02:48:04.862-07:00Comments on Machine Phase: How to install GROMACS on windows vista 64Tomhttp://www.blogger.com/profile/01639800769521054448noreply@blogger.comBlogger65125tag:blogger.com,1999:blog-3060898714439566244.post-68354385255286249472016-04-11T09:08:26.618-07:002016-04-11T09:08:26.618-07:00Dear Dr. Tom,
Your post on Gromacs installation ...Dear Dr. Tom, <br /><br />Your post on Gromacs installation in Windows vista was great!!!<br /><br />I am new to install Gromacs in windows 7, i encountered with a problem when installed fftw-3.3.4 in cygwin (64-bit). The returned result showed "no such directory or file" from the bash when i typed in "./configure..".The folder (directory of fftw is C:/) May i know what are the mistakes? Your response is much more appreciated!!! Looking forward to hearing from you. Thank you. <br /><br />Tan SH <br />siyang13@gmail.comsiyang zhaohttps://www.blogger.com/profile/11541515700298156278noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-11547312141103557512015-12-11T02:42:05.005-08:002015-12-11T02:42:05.005-08:00Hello,
I have successfully installed FFTW and Gro...Hello,<br /> I have successfully installed FFTW and Gromacs as suggested, but the unable to run the luck command.Anonymoushttps://www.blogger.com/profile/15795271263894080447noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-31857920590252814872015-11-26T00:39:59.918-08:002015-11-26T00:39:59.918-08:00Hello sir,
I am Rajan, doing Ph.D. from central un...Hello sir,<br />I am Rajan, doing Ph.D. from central university of Rajasthan. I have to install Gromacs on my CENTOS 7 operating system. Kindly give me the instruction that how can i install it on same platform<br /><br />Regards<br />Rajan<br />Email: rkpandey255@gmail.comAnonymoushttps://www.blogger.com/profile/08432615777300250193noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-9179587817256283482013-02-26T18:32:10.958-08:002013-02-26T18:32:10.958-08:00i am using windows7 64 bit machine
downloaded fft...i am using windows7 64 bit machine<br /><br />downloaded fftw-3.3.3-dll64, unzipped in folder C:\Packages\fftw<br /><br />cd /cygdrive/c/Packages/fftw<br /><br />./configure --prefix=/cygdrive/c/Packages/fftw --enable-float<br /><br />ERROR -bash: ./configure: No such file or directory<br /><br />Then i tried <br />./configure --enable-threads --enable-sse --enable-float<br /><br /> <br />ERROR -bash: ./configure: No such file or directory<br /><br />what can be doneNitin Sharmahttps://www.blogger.com/profile/12412585777193496053noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-91062724950720339282013-02-26T18:31:58.803-08:002013-02-26T18:31:58.803-08:00This comment has been removed by the author.Nitin Sharmahttps://www.blogger.com/profile/12412585777193496053noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-74763767812221039422011-12-20T07:30:41.288-08:002011-12-20T07:30:41.288-08:00Hi,
I am using Windows 7 and have followed the ...Hi,<br /> I am using Windows 7 and have followed the given instructions for installing Gromacs but while opening the Cygwin Terminal an error is occuring - could not load icon from '/Cygwin-Terminal.ico'Aparajeohttps://www.blogger.com/profile/17083126126677365590noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-68405246003565523822011-11-11T00:22:20.242-08:002011-11-11T00:22:20.242-08:00Thank you for the info. It sounds pretty user frie...Thank you for the info. It sounds pretty user friendly. I guess I’ll pick one up for fun. thank u <a href="http://www.roxycomputers.com.au/computer-reformat.htm" rel="nofollow">Window Installation Melbourne</a>sandhiyahttps://www.blogger.com/profile/03143516437153944655noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-58758046480856816322011-06-17T06:47:46.966-07:002011-06-17T06:47:46.966-07:00Hi
I am installing Gromacs in Ubuntu 10.10
using f...Hi<br />I am installing Gromacs in Ubuntu 10.10<br />using fftw-3.0.1 and Gromacs-3.3.1 on my Advent 4211. Who can help me please to not obtain the message '***No targets specified and no makefile found. Stop' in the install of Gromacs at 'make' stage as mentionned below.<br /><br />Procedure:<br />FFTW for Linux<br /> 1. cd fftw-3.0.1<br /> 2. ./configure --enable-float --enable-threads<br /> 3. make<br /> 4. su (Type in your root password and hit the enter button)<br />in this step i have used sudo because i did not know how to get root password.<br /> 5. make install<br /><br />Now to do the double precision version, we need to clean up the tree.<br /><br /> 1. make distclean<br /> 2. ./configure --enable-threads<br /> 3. make<br /> 4. make install<br /><br />So now we have FFTW package installed on our system.<br /><br />Install Gromacs-3.3.1<br /><br /> 1. cd gromacs-3.3.1<br /><br /> 2. ./configure --disable-float (For double precision)<br /> 3. make (here my problem. i receive:<br />***No targets specified and no makefile found. Stop) <br /> 4. sudo -s (This is for Mac)<br /> su (This is for Linux)<br /> 5. make installNabilhttps://www.blogger.com/profile/09439818076179569597noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-26984808640867318802011-06-17T06:47:31.902-07:002011-06-17T06:47:31.902-07:00Hi
I am installing Gromacs in Ubuntu 10.10
using f...Hi<br />I am installing Gromacs in Ubuntu 10.10<br />using fftw-3.0.1 and Gromacs-3.3.1 on my Advent 4211. Who can help me please to not obtain the message '***No targets specified and no makefile found. Stop' in the install of Gromacs at 'make' stage as mentionned below.<br /><br />Procedure:<br />FFTW for Linux<br /> 1. cd fftw-3.0.1<br /> 2. ./configure --enable-float --enable-threads<br /> 3. make<br /> 4. su (Type in your root password and hit the enter button)<br />in this step i have used sudo because i did not know how to get root password.<br /> 5. make install<br /><br />Now to do the double precision version, we need to clean up the tree.<br /><br /> 1. make distclean<br /> 2. ./configure --enable-threads<br /> 3. make<br /> 4. make install<br /><br />So now we have FFTW package installed on our system.<br /><br />Install Gromacs-3.3.1<br /><br /> 1. cd gromacs-3.3.1<br /><br /> 2. ./configure --disable-float (For double precision)<br /> 3. make (here my problem. i receive:<br />***No targets specified and no makefile found. Stop) <br /> 4. sudo -s (This is for Mac)<br /> su (This is for Linux)<br /> 5. make installNabilhttps://www.blogger.com/profile/09439818076179569597noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-91633043317453671152011-06-05T14:20:18.929-07:002011-06-05T14:20:18.929-07:00hi Tom,
Thanks
i have installed it but unfortunate...hi Tom,<br />Thanks<br />i have installed it but unfortunately, it did not work properly.<br />As you said i need to install it in Linux.Nabilhttps://www.blogger.com/profile/09439818076179569597noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-59844240602986628462011-06-05T09:58:33.671-07:002011-06-05T09:58:33.671-07:00Yes, you can do both. Also I'm not going to ma...Yes, you can do both. Also I'm not going to maintain this thread anymore. In the future I recommend you use gromacs on linux. It is very easy to install and there is a lot more documentation for it.Tomhttps://www.blogger.com/profile/01639800769521054448noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-4284716940941734122011-06-05T01:35:39.937-07:002011-06-05T01:35:39.937-07:00Hi again
how can i install gromacs on win XP?
than...Hi again<br />how can i install gromacs on win XP?<br />thank's a lotNabilhttps://www.blogger.com/profile/09439818076179569597noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-46032326240634664342011-06-05T01:33:26.788-07:002011-06-05T01:33:26.788-07:00hi
i am trying to install gromacs on vista 32.
do ...hi<br />i am trying to install gromacs on vista 32.<br />do you think it will work?Nabilhttps://www.blogger.com/profile/09439818076179569597noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-47954935912684197232011-05-31T17:29:39.004-07:002011-05-31T17:29:39.004-07:00Hi
I am trying to install gromacs on windows but...Hi <br /><br />I am trying to install gromacs on windows but the ./configure for gromacs says that it is not able to find libraries for fftw3...I clearly installed fftw properly ...please help <br /><br />thanks in advance <br /><br />mahesh@lt3REg0https://www.blogger.com/profile/03191051410272618920noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-1200371898929878782011-05-26T02:09:45.590-07:002011-05-26T02:09:45.590-07:00Hi,
if anyone is having the same problem as MH an...Hi,<br /><br />if anyone is having the same problem as MH and did with gromacs 4.5.4 under Vista: Configuring gromacs with --disable-shared instead of --enable-shared solved the problem for me, although this consumes some more memory than building the DLL. <br /><br />Best, Georggeorg.zeplinhttps://www.blogger.com/profile/16400764777051033070noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-12808153166859282282011-05-02T05:32:37.784-07:002011-05-02T05:32:37.784-07:00Hello Tom,
having the same problem as MH, I have ...Hello Tom,<br /><br />having the same problem as MH, I have found an additional warning of the make that may help solving the problem:<br /><br /><i>"*** Warning: This system can not link to static lib archive /usr/local/lib/libfftw3f.la.<br />*** I have the capability to make that library automatically link in when<br />*** you link to this library. But I can only do this if you have a<br />*** shared version of the library, which you do not appear to have."<br /></i><br /><br />After that warning there is a bunch of warnings, with unresolves symbols like:<br /><i>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2a7): undefined reference to `_fftwf_execute_dft_c2r'</i><br />I don't know pretty much on compiling, but the error seems to be related to fftw. I have tried fftw 3.2.2 and gromacs 4.5.4.<br /><br />Best, Georggeorg.zeplinhttps://www.blogger.com/profile/16400764777051033070noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-50972184020930497282011-03-22T17:20:28.568-07:002011-03-22T17:20:28.568-07:00in linux, just type
sudo apt-get install gromacs ...in linux, just type <br />sudo apt-get install gromacs <br /><br />to install gromacs, read this too<br />http://www.gromacs.org/Documentation/ManualTomhttps://www.blogger.com/profile/01639800769521054448noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-37296415199151908822011-03-22T14:44:49.225-07:002011-03-22T14:44:49.225-07:00Hi Tom
I am a student and i want to learn GROMACS....Hi Tom<br />I am a student and i want to learn GROMACS. I am not able to follow the instructions or may be i missed something. <br />Can u help me out with something that is easy to use. I have installed fedora13 on my system n have installed fftw, gromacs too.<br />Do not know how to operate GROMACS.<br /><br />Any link that has commands to operate GROMACS, then plz send me.Unknownhttps://www.blogger.com/profile/14935657518283290992noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-28673303950173708222011-02-10T14:00:21.275-08:002011-02-10T14:00:21.275-08:00Yes, the problem is that I don't see "sha...Yes, the problem is that I don't see "share" folder in D:\cygwin\usr\local\gromacs-4.5.3<br />And I am installing it on windows 7.<br /><br />Thanks,<br />MajidUnknownhttps://www.blogger.com/profile/12944042689927723281noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-19877626942082684712011-02-10T08:54:20.533-08:002011-02-10T08:54:20.533-08:00You do not have a shared folder then?
C:\cygwin\u...You do not have a shared folder then?<br /><br />C:\cygwin\usr\local\gromacs\share\gromacs\tutor<br /><br />Don't reinstall just yet, but I'm not sure what the problem is. Make sure the folder is not hidden, and keep looking around. If you don't find it, email me.<br /><br />TomTomhttps://www.blogger.com/profile/01639800769521054448noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-44072221606015141692011-02-09T22:12:32.761-08:002011-02-09T22:12:32.761-08:00Dear Tom,
I have figured out my earlier problem, ...Dear Tom,<br /><br />I have figured out my earlier problem, but I am facing a new one. <br /><br />While trying to run the gromacs demo, I realized that its not present in cygwin folder. When I go into cygwin/usr/local/gromacs, I only see bin, include and lib folders. Could you tell me how can I fix that problem? Can I reinstall gromacs?<br /><br />Thanks,<br />MajidUnknownhttps://www.blogger.com/profile/12944042689927723281noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-35700983652165553172011-02-09T18:11:46.262-08:002011-02-09T18:11:46.262-08:00Just to clarify my previous comment, I was trying ...Just to clarify my previous comment, I was trying to run gromacs after following all the steps in your blog. I was following the instructions given on http://tunicata.techfak.uni-bielefeld.de/TOBIX/tutorials/gromacs/online/getting_started.html. And in the first step it asks you to start C shell with tcsh command, which I am unable to find.<br /><br />Thanks for your time,<br />MajidUnknownhttps://www.blogger.com/profile/12944042689927723281noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-63902711575047046712011-02-09T18:08:36.084-08:002011-02-09T18:08:36.084-08:00Dear Tom,
Thanks to your nice blog, I have appare...Dear Tom,<br /><br />Thanks to your nice blog, I have apparently installed the cygwin, and Gromacs successfully. However, As you said, we need to install "tcsh" package. Now, I installed cygwin 1.7, but I couldn't find "tcsh" in any mirror. Is it supposed to be in development package? I do have a a file named "tclsh". Could it be the same thing?<br /><br />Thanks,<br />MajidUnknownhttps://www.blogger.com/profile/12944042689927723281noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-13810595156439018302010-06-07T13:47:23.980-07:002010-06-07T13:47:23.980-07:00there should be a log file, config.log, that tells...there should be a log file, config.log, that tells you more. Also just past preprocessor "/lib/cpp" fails sanity check into google. There is a lot of info.<br /><br />Best of luck,<br /><br />TomTomhttps://www.blogger.com/profile/01639800769521054448noreply@blogger.comtag:blogger.com,1999:blog-3060898714439566244.post-39159581604960961882010-06-06T20:47:00.221-07:002010-06-06T20:47:00.221-07:00Hi Tom,
Your post is linked as a resource for ins...Hi Tom,<br /><br />Your post is linked as a resource for installing Gromacs in Windows. It is a good start.<br /><br />I am having problems installing serial Gromacs with Windows 7. I got Cygwin, installed the packages mentioned in your blog under Devel inluding gcc and gcc-f77. I got fftw-3.2.1 and did it succesfully with Cygwin. I downloaded gromacs-4.0.7. But when I try to run $ ./configure --enable-shared LDFLAGS="-L/usr/local/lib" what appears is an error: C++ preprocessor "/lib/cpp" fails sanity check.<br /><br />I did another configure run with the line $ ./configure --enable-shared LDFLAGS="-L/usr/local/lib" CPPFLAGS="-I/usr/local/include". Again, I get the same error. <br /><br />How to I correct the problem. Thanks. BeeBernhttps://www.blogger.com/profile/05223883363188226482noreply@blogger.com