AMBER Archive (2008)

Subject: Re: AMBER: problem in starting sander

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jun 08 2008 - 14:53:33 CDT

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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