Re: [AMBER] constant pressure simulation

From: kirtana S <>
Date: Fri, 5 Jul 2013 11:05:00 -0700

Dear Amber Users,

Following is the frcmod file
H1 1.0
OH 16.
CT 12.
HO 1.

  H1 1.3770 0.0150
  OH 1.7210 0.2104
  CT 1.9080 0.1094
  HO 0.0 0.0

I am using methanol to solvate my polymer chain. I have attached the
library file used for my simulations. When I perform constant pressure
simulations of polymer in methanol box at 300K the box expands. So now I
have used only methanol in a box constructed with the following commands in
xleap using the library file.
source leaprc.ff03
loadamberparams methanol.frcmod

setbox a vdw 2
saveamberparm a M.prmtop M.inpcrd

The library file, prmtop and inpcrd file are attached.

My simulation run is minimization, constant volume simulations where I heat
to 300K followed with constant pressure run

   maxcyc=10000, ncyc=1000,

   ntxo=1, ntrx=1,
   ntpr=500, ntwx=500, ntwe=500,
   nstlim=300000, temp0=300.0,
   ntc=2, ntf=2,tol=0.00001,
   ntx=1, irest=0,
 type='TEMP0', istep1=0, istep2=200000, value1=0.1, value2=300.0,
 type='TEMP0', istep1=200001,istep2=300000,value1=300.0, value2=300.0,
 &wt type='END',
RES 1 1743

   ntxo=1, ntrx=1,
   ntpr=500, ntwx=500, ntwe=500,
   nstlim=500000, temp0=300.0,
   ntc=2, ntf=2, tol=0.00001,
   ntx=5, irest=1,

I want to obtain the heat of vaporization using Upot from my simulations.
Please let me know where is the problem.


On Fri, Jul 5, 2013 at 5:35 AM, David A Case <>wrote:

> On Thu, Jul 04, 2013, kirtana S wrote:
> >
> > I am performing a constant pressure simulations with a methanol box . My
> > system blows up i.e during the constant pressure run the box expands.
> > Please suggest
> There is way too little information here for anyone on the list to be of
> much
> help. For example, we don't know which force field you used, how you
> created
> the initial coordinates, how much the box expanded, what temperature you
> used,
> and so on.
> ...dac
> _______________________________________________
> AMBER mailing list

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Received on Fri Jul 05 2013 - 11:30:03 PDT
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