[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

[Justin Lemkul]

On 3/23/15 11:24 AM, Alex wrote:
> Hey Justin,
>
> Thanks. I am not entirely sure I understand your suggestion, because
> this will clearly work if nothing else is added to the system (it
> seems to be equivalent to that CNT guide). The problems start after I add
> water, i.e. "duplicate [ defaults ]" from grompp and such. In the meantime, I will
> try the earlier suggestion and add the bonded definitions on top of
> what was suggested.
>

If you're introducing a new [defaults] directive, then whatever you're doing is 
breaking the required force field format.  Chapter 5 is your best friend here. 
You say you want some custom parameters and that you're having issues with 
implementing new parameter into existing force fields, so I'm telling you that 
the best approach (in my mind) is to do something simple.  Something that you 
can write in a few lines (for a CNT you have a single C type and I can count the 
bonded parameters on one hand).  Make sure that works.  Then worry about making 
it more complicated.  But at that point, you're just adding more [atomtypes] and 
[bond|angle|dihedraltypes], nothing more.  You only ever have one [defaults] - 
these are the master instructions for the shape of the functional form and how 
the force field is interpreted.

Canary in the mineshaft - get the CNT working alone.  Make sure you understand 
everything about that.  Because at that point, you've done most of the hard work 
and everything is just an addition to it.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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