AMBER Archive (2008)

Subject: RE: AMBER: problem in starting sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Jun 08 2008 - 17:30:17 CDT

Hi Qiuting

 

What exactly do you mean by " I can't see any output result in
6lyzwatmin1.out even the job run for a long time"?

 

Do you not get any output file at all? Or the output file exists, contains
some info but only effectively start up information? If so then what is the
last line in the output file?

 

Normally you can get this problem when you have a gas phase or implicit
solvent prmtop and inpcrd file but set ntb=1. Sander then hangs trying to
read the box info from the inpcrd file when that info doesn't exist. So
check your prmtop and inpcrd file contain box information and are setup for
a periodic system.

 

Failing that please clarify what exactly the problem is. Also do all the
test cases run fine?

 

All the best

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Qiuting Hong
Sent: Sunday, June 08, 2008 11:26 AM
To: amber_at_scripps.edu
Subject: AMBER: problem in starting sander

 

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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