Tuesday, April 28, 2009

multiwall carbon nanotube & GROMACS

Force constants:

Bonds 47890 KJ/mol/nm^2
Angle 400 KJ/mol/rad^2
Dihedral 167.36 KJ/mol/rad^2


alexkiev said...

Hi, it is amazing )))) I've followed your manual for installing gromacs on cygwin several monthes ago. And I'm here again ))) Can I ask you a question: what means bond force, angle force...? have you asigned it on x2top step or latter? I must reproduce this process: "To obtain a PMF
with respect to the rotation of the dihedral angle, C40–C30–O30–
HO30, we employed the umbrella sampling technique, using 14
windows in the range of 50–180 . The force constants
of the umbrella potential in those windows were set to
10.0 kcal/mol rad2." I don't understand how to do this, this is not a simple COM pull, angle forceing is unclear for me. Can you help me? (rayevsky85@gmail.com)

Tom said...


These are the energy parameters for the force field. For a little more in depth explanation, look here:


I added these parameters to the oplsa force field files in the gromacs/top directory. Look at this post for a better explanation on how to add them:


I think you can override the values in x2top, but add them to the force field

alexkiev said...

Thank you for instantaneous response. So correct me if I'm wrong. To obtain PMF in this way, as it was described in the part of article mentioned above, I need to alterate some parameters of my forcefield (amber99) and start a new simmulation. As a result I'll see, that this amendment will cause changes in behaviour of atoms included in C40–C30–O30–
HO30 dihedral...Now it is clear, thank you very much for explanation. But what about "using 14
windows in the range of 50–180" and constants in them? Is this the same process?

Tom said...

I'm afraid I am not familiar enough with umbrella sampling to really know the answer. Sorry.


alexkiev said...

Ok, that's all right ))))) in any case your advices are very usefull. And I think not only for me. Thank you, guru!

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