AMBER Archive (2004)

Subject: Re: AMBER: Sander

From: David A. Case (
Date: Mon Aug 09 2004 - 11:57:40 CDT

On Mon, Aug 09, 2004, sachin patil wrote:

> I am running an MD simulation with nonperiodic
> conditions, having added a watercap 30 A in radius.I
> have two such similar systems which only differ in
> that I have manually added extra water molecules to
> one of these.
> &cntrl
> nstlim=100000,dt=0.002,
> cut=6,ntb=0,
> temp0=298,ntt=4,
> irest=1,ntx=5,nmropt=1,
> ntr=1,tautp=2.0,
> ntf=2, ntc=2,
> ntwx=500, ntpr=500, ntwr=5000,
> nrespa=1,
> &end
> &wt type='END'
> &end
> DISANG=./distfinal.rst
> group input for restrained atoms
> 2.0
> RES 1 475

You should set a "cap" potential to keep the waters from "evaporating"
off into space...this is what causes the halts you see. I would recommend
setting ntt=3 (Langevin dynamics) for temperature control. Setting cut=6
is just going to lead to very bad results...set this as large as you can
afford (at least 12 Ang.). Equilibrate first with dt=0.001 until you
have a stable simulation.

...good luck...dac

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