<div>Dear Bob Johnson and other users,</div>
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<div>I am attempting to set up some infinite carbon nanotube simulations. To begin, I want to take a single nanotube with some argon inside and try to simulate it with GROMACS with PBC in the axial direction (it appears I need to use pbc=full).
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<div>So I have a lot of experience with NAMD, but really nothing with GROMACS</div>
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<div>So far I can use x2top to generate a topology file from a pdb</div>
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<div>It seems to work ok as I can make it output all of the dihedrals and seems to match up with what I would get with a psf for NAMD. </div>
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<div>I am a bit confused on how to include my forcefield with the simulation and to generate the proper *gro file. The x2top generated *top file seems to not have the proper mass for Argon and also doesn't include the parameters for the forcefield. I attempted to generate my own forcefield files in the top directory (
ffCNT.itp, ffCNTnb.itp, etc, etc.). It seems from reading the mailing list that I don't need to do this and can just use my pdb file and topology file generated from x2top to start the simulation. </div>
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<div>How, then would I include my CNT force field (A morse bond, cosine angle, and RB dihedral)? I have created these files already as I stated above. Could I just include this as a separate *itp file as the methanol example shows? Does this file then override the *top file? So I could include it as #include "
CNT.itp" or something in the *top file? This is my main question. I am also a bit confused on the format of this as I don't really have a "molecule" as for methanol, just atoms for the carbon and argon atoms.
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<div>Second question (and very naive). Can you start a MD simulation with GROMACS without a *gro file and just a *pdb? </div>
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<div>I realize that my message here is a bit naive, so I hoping someone will be nice enough to overloook my lack of general knowledge about GROMACS :)</div>
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<div>Thanks</div>
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<div>Joshua Moore</div>
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<div>PS I address Bob Johnson as he seems to be the expert on nanotubes in GROMACS :)<br clear="all"><br>-- <br>------------------------------------------------<br>Joshua D. Moore<br>Graduate Student<br>North Carolina State University
<br>Dept. of Chemical and Biomolecular Engineering<br>Box 7905 Centennial Campus<br>Engineering Building I<br>911 Partners Way<br>Raleigh, NC 27695-7905<br>Phone: (919) 513-2051<br>Fax: (919) 513-2470<br>Email: <a href="mailto:jdmoore@unity.ncsu.edu">
jdmoore@unity.ncsu.edu</a><br>------------------------------------------------ </div>