AMBER Archive (2004)

Subject: Re: AMBER: Sander

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Mon Aug 09 2004 - 13:26:20 CDT

Dear David A. Case,
 So, for a cap size of 1342 atoms what restrain
potential I shall use so that the water molecules dont
evaporate?
 Thanks in advance

Sachin Patil

 --- "David A. Case" <case_at_scripps.edu> wrote:
> 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
> > LISTOUT=POUT
> > group input for restrained atoms
> > 2.0
> > RES 1 475
> > END
> > END
>
> 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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