AMBER Archive (2008)

Subject: AMBER: problem in starting sander

From: Qiuting Hong (qiutinghong_at_gmail.com)
Date: Sun Jun 08 2008 - 13:25:43 CDT

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

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