Re: [AMBER] constant pressure

From: kirtana S <skirtana4.gmail.com>
Date: Mon, 5 Dec 2011 18:18:11 -0500

Thank you all for the help and suggestion made .

According to the suggestions of Prof Duan after running constant volume and
then using single processor due to density of my system in constant
pressure the simulation runs with some statements as
check COM velocity, temp: 0.000220 0.00 (Removed) in my out file .
are these alright to proceed. My constant pressure input file below

&cntrl
imin=0, ntx=5,
irest=1, ntxo=1,tempi=50.0,
ntf=1, ntc=1,
ntpr=1000, ntwx=1000, ntwe=1000,
nstlim=1500000,tautp=1, temp0=50.0,
dt=0.0005, nscm=100,
ntb=2,ntp=1,
ntt=1, nsnb=20,
&end

My other question is I have equilibrated the system at 50K . Whereas my MD
run is to be done at 300K . So should I repeat these steps to gradually
raise the temperature to 300K at constant volume. Again while heating
should I need to have restraints on the residues (or solute) I am using the
present run for a bigger system , I can send the output files again if
required.

Kirtana

On Mon, Dec 5, 2011 at 8:19 AM, David A Case <case.biomaps.rutgers.edu>wrote:

> On Sun, Dec 04, 2011, Brian Radak wrote:
>
> > Minimization usually (always?) ignores PBCs.
>
> This is not correct; just noting that to prevent further confusion in a
> long
>
> There should be no need to minimize between doing a constant volume and and
> constant pressure equilibration. In fact, the safest thing to do is to
> make sure irest=1 (so you are continuing from a previous run), and that the
> only change to the input is from ntb=1,ntp=0 --> ntb=2,ntp=1. In the
> constant
> pressure run, set ntpr=1 and nstlim=50, and make sure that the energies at
> the
> first step of the constant pressure run match those at the last step of the
> NVT equilibration. [I'm wondering if there is some problem with how you
> are
> naming the input files--be sure that restart file from the previous step is
> indeed used as the input file for the next step.]
>
> ....dac
>
>
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Received on Mon Dec 05 2011 - 15:30:02 PST
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