2011/11/7 hai wei <weihy61.gmail.com>
> "My recommendation is to avoid using belly, and just use ntr=1 restraints."
>
> while I read most of papers regards Graphene sheet or Carbon Nanotube
> simulation, They all said, keep the carbon atom of graphene sheet/CNT
> fixed.. If I just use ntr=1 to *restrain* the graphene sheet, the graphene
> is deformed，so the only way here is to use ibelly to *constrain* to keep
> the carbon atom of graphene sheet/CNT fixed. Do you mean that wrong MD
> simulaiton will come out using belly? I am confused.
>
If the graphene sheet is really deformed using even a force constant of 10
kcal/mol/Å**2, then I'm guessing that the force constant is not being
applied like you're expecting. If it is, then it likely means that your
graphene sheet is poorly parametrized (because "natural" forces are
distorting it despite the strength of the restraints).
The output file should print details about which atoms are constrained (try
using a restraintmask instead of the group input if you're using sander,
since then you can compare with ambmask to make sure you're restraining the
right atoms), and the restraint energy should give you clues as to what is
happening.
HTH,
Jason
> haiya
>
>
> haiya
>
> 2011/11/7 David A Case <case.biomaps.rutgers.edu>
>
> > On Mon, Nov 07, 2011, hai wei wrote:
> >
> > > ”Third, 500 is too strong a force constant for most purposes. Consider
> > > using a value about two orders of magnitude smaller.“
> > >
> > > If I want to keep Graphene sheet Constrain in the MD simulaiton, is 500
> > > still too much?
> >
> > Yes....dac
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Nov 07 2011 - 17:30:03 PST
