AMBER Archive (2002)

Subject: Re: problem in MD

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Tue Aug 27 2002 - 20:40:06 CDT

Did you do anything else to the sytem after
creating it? Minimization, etc?
Also, please provide more of the output, such
as first step energies. How long does it run (in
# steps) before stopping?
CS

----- Original Message -----
From: "Xiang Mao" <xmao_at_iris.sipp.ac.cn>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, August 27, 2002 8:05 PM
Subject: problem in MD

> Hello, everyone:
> I met a problem when I was doing MD using sander_classic. The
> input file is the following:
> -=----------------------------------------
> # Heat system using Berendsen alg. (10ps), dist dep dielc
> &cntrl
> t= 0.0 ,
> ig= 739972 ,
> imin = 0, ntx = 1, ntpr = 50, ntwx = 50,
> ntwe = 0,
> ntcm = 1, ndfmin = 6, nscm = 50,
> ntwxm = 0, ntwem = 0, ntwprt = 0,
> ntf = 2,
> ntb = 1, ntp = 0, pres0 = 1.0,
> ntc = 2, tol = 1.0e-4,
> nsnb = 25,
> scee = 1.2,
> idiel = 0, dielc = 4.0,
> nrun = 1, nstlim =5000,
> dt =.002,
> irest = 0, init = 3,
> tempi = 0.0, temp0 =300., ntt = 1, dtemp = 4.,
> tautp = 1.0, tauts = 0.2, taup = 1.0,
> iewald = 0,
> nmropt = 0, ntr = 0,
> &end
> ----------------------------------------
> and the output file says that coordination resetting can not be
> accomplised, the deviation is too large.
>
> My system is a protein soaked in a cubic water box, so I wonder if
> you could help me find the reasons for that problem. Thanks in advance.
>
>
> Regards,
> xiang mao
>
>