Dr. Case,
Thank you very much for the explanation. I would like to keep the nscm so
that at least the translational motion is removed over the simulations.
Below is my code for the NPT simulation,and it was run using PMEMD engine.
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 12, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 2,
nstlim = 1000000, dt = 0.002,
ntpr = 1000, ntwx = 1000, ntwr = 1000
/
&ewald vdwmeth=0, verbose=2
/
END
Dr. Cerutti or any other Amber developers,
Thank you for looking into the code.
Best,
Mo
On Mon, Oct 29, 2012 at 10:10 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Oct 29, 2012, Mo Chen wrote:
> >
> > It seems the Molecular Virial is the 3d stress/pressure tensor matrix.
>
> I think this is wrong. The pressure is determined by a combination of the
> virial and kinetic energy terms. See code around line 911 of runmd.F90.
>
> Athough sander computes the full virial tensor (I think for conversion back
> from non-orthogonal unit cells), it only computes the diagonal components
> of
> the pressure tensor. I think extra coding would be required to get more.
>
> > However, my system is a cubic box, and the output shows that the
> > stress/pressure tensor matrix is not symmetric. I found in Amber Manual
> > that when ncsm is applied to a periodic system, it only remove the
> > translational COM motion, but not the rotational COM motion.
>
> This is correct. There is no way to remove rotational motion in an
> infinite
> periodic system, (and not way for such components to build up in the first
> place.) If you are concerned about this, you can set nscm to zero to turn
> this off.
>
> cc-ing to Dave Cerutti, who has looked into this stuff more than I have.
>
> ...dac
>
>
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Received on Mon Oct 29 2012 - 13:00:04 PDT
