Re: [AMBER] constant pressure simulation

From: kirtana S <skirtana4.gmail.com>
Date: Fri, 5 Jul 2013 11:05:00 -0700

Dear Amber Users,

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


NONB
  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
loadoff methanol.off

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

cntrl
   imin=1,
   ntb=1,
   cut=10.0,
   maxcyc=10000, ncyc=1000,
   ntt=0,
&end

&cntrl
   imin=0,
   ntxo=1, ntrx=1,
   cut=12.0,tempi=0.1,
   ntpr=500, ntwx=500, ntwe=500,
   nstlim=300000, temp0=300.0,
   dt=0.002,dielc=33,
   ntc=2, ntf=2,tol=0.00001,
   ntx=1, irest=0,
   ntb=1,tautp=2,
   ntt=1,
   nmropt=1,ntr=1,
 /
 &wt
 type='TEMP0', istep1=0, istep2=200000, value1=0.1, value2=300.0,
 /
 &wt
 type='TEMP0', istep1=200001,istep2=300000,value1=300.0, value2=300.0,
 /
 &wt type='END',
 /
GROUP FOR CONSTRAINTS
 0.5
RES 1 1743
END
END

 &cntrl
   imin=0,
   ntxo=1, ntrx=1,
   cut=12.0,tempi=300.0,
   ntpr=500, ntwx=500, ntwe=500,
   nstlim=500000, temp0=300.0,
   dt=0.002,dielc=33,
   ntc=2, ntf=2, tol=0.00001,
   ntx=5, irest=1,
   ntb=1,tautp=1,
   ntt=1,
  /

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

Thanks
Kirtana








On Fri, Jul 5, 2013 at 5:35 AM, David A Case <case.biomaps.rutgers.edu>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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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