On 11/13/13 10:39 AM, Atila Petrosian wrote:
Dear Justin

Thanks for your reply.

In your previous setup, you were effectively trying to use CHARMM27 + some other
force field related to the CNT.  You can't do that.

Thus, Gromacs is not appropriate for systems containing cnt.
Is my deduction true?

Of course not. People simulate CNTs with Gromacs all the time. You just didn't construct the force field properly.

In my case, peptid + cnt + water molecules, what is your suggestion?

Please guide me and explain more. How to do MD simulation of my system
by gromacs?

You have missing parameters in the .top/.itp file. You have those parameters already in ffbonded.itp for the CNT. As long as those parameters are compatible with the peptide force field (CHARMM27), then you just need to add those parameters. Again, that may be as simple as adding #include "cntffbonded.itp" of whatever it is to the .top file after the #include statement for the parent force field. Your only problem was #including another force field that re-defined a [defaults] directive. That is syntactically illegal. Nothing else was inherently problematic, unless you're mixing incompatible force fields, but I haven't seen any evidence of that.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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