AMBER Archive (2008)

Subject: Re: AMBER: problem in starting sander

From: Qiuting Hong (qiutinghong_at_gmail.com)
Date: Sun Jun 08 2008 - 16:52:34 CDT

I try ntpr=1. Problem doesn't solve. One thing I forgot to mention is sander
doesn't give me the 6lyzwatmin1.rst file.

On Sun, Jun 8, 2008 at 12:53 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> maybe try setting ntpr=1
>
> On Sun, Jun 8, 2008 at 2:25 PM, Qiuting Hong <qiutinghong_at_gmail.com>
> wrote:
> > Dear all,
> >
> > I am trying to run MD for lysozme in explicit water. However, I have a
> > problem in starting sander. I never has a problem like this before.
> > Below is what I did:
> >
> > [258] castalia.sfsu.edu>$AMBERHOME/exe/sander -O -i mdin \
> > ? -o 6lyzwatmin1.out -p 6lyzwat.prmtop -c 6lyzwat.inpcrd \
> > ? -r 6lyzwatmin1.rst -ref 6lyzwat.inpcrd
> > There is no error message, and when I check by keying in top, it gives me
> >
> > 10:56:50 up 8 days, 16:11, 10 users, load average: 0.91, 0.73, 0.35
> > 85 processes: 84 sleeping, 1 running, 0 zombie, 0 stopped
> > 11:05:58 up 8 days, 16:21, 10 users, load average: 0.99, 0.83, 0.52
> > 86 processes: 83 sleeping, 3 running, 0 zombie, 0 stopped
> > CPU states: cpu user nice system irq softirq iowait idle
> > total 50.2% 0.0% 0.0% 0.0% 0.0% 0.0% 49.7%
> > cpu00 0.4% 0.0% 0.0% 0.0% 0.0% 0.0% 99.5%
> > cpu01 100.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
> > Mem: 16212488k av, 1276012k used, 14936476k free, 0k shrd,
> 172556k
> > buff
> > 349472k active, 426068k inactive
> > Swap: 4096564k av, 0k used, 4096564k free 521588k
> > cached
> > PID USER PRI NI SIZE RSS SHARE STAT %CPU %MEM TIME CPU COMMAND
> > 6401 qiuting 25 0 988 988 736 R 49.9 0.0 6:29 1 sander
> > 6292 qiuting 15 0 18536 18M 13976 S 0.2 0.1 0:00 0 kdeinit
> > 1 root 15 0 524 524 456 S 0.0 0.0 0:07 0 init
> > 2 root RT 0 0 0 0 SW 0.0 0.0 0:00 0
> > migration/0
> > 3 root RT 0 0 0 0 SW 0.0 0.0 0:00 1
> > migration/1
> > It seams sander is running, however, I can't see any output result
> > in 6lyzwatmin1.out even the job run for a long time.
> > My input file is
> > 6lyzwat: minimize solvent +ions
> > &cntrl
> > imin =1,
> > maxcyc =1000,
> > ncyc =500,
> > ntb =1,
> > ntr=1,
> > cut =12
> > /
> > Keep 6lyz frozen
> > 500
> > RES 1 129
> > END
> > END
> >
> > I try in both amber8 and amber9, and I meet the same problem. Can
> somebody
> > help me out?
> >
> > Thank you.
> >
> > Qiuting
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
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