Thanks, I am gonna check the outfile.
haiya
2011/11/8 Jason Swails <jason.swails.gmail.com>
> 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 - 19:30:02 PST
