AMBER Archive (2003)

Subject: Re: water box distortion

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Fri May 23 2003 - 16:21:33 CDT

Try adding "iwrap = 1" to your input file.

jim

On Fri, 23 May 2003, GUILLERMINA L ESTIU wrote:

> Hi,
> I am running simulations (amber 7) for a sistem of 2500 residuos (50000 after
> building the water box)
> I am trying to equilibrate the system. As a way of starting, I am heating only
> the solvent, but the water box is not kept "cubic"
>
> Can someone tell me waht is wrong in this input file?
>
> molecular dynamics run
> &cntrl
> imin=0, irest=1,
> ntx=5, ntr=1,
> lastist=9000000,
> lastrst=12000000,
> tempi= 300.,
> ntt=1, temp0=300.0, tautp=0.5,
> ig=71277, heat=0.0,
> ntb=1, ntc=2, tol= 0.00001, ntf=2,
> scee=1.2, dt=0.0005,
> cut=9.0, nsnb=25,
> nstlim=100000,
> vlimit= 20
> ntwe=50, ntwx=50, ntpr=10, ntwr=100,
> &end
> Group input for restrained atoms
> 10000.0
> RES 1 2479
> END
> END
>
> Dr Guillermina Estiu
> Chemistry Department
> Pennsylvania State University
> PA 16802
> 

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