AMBER Archive (2008)

Subject: RE: AMBER: VMD Movie 3

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 29 2008 - 13:47:52 CDT

Hi Pat,

 

You should have ended up with 1000 frames in your mdcrd file. I suspect
therefore that it is corrupt in some way. When you load it into VMD take a
look in VMD's console window and see if there are any error messages
printed. You may also want to run it through ptraj (calc an RMSD say) and
see if ptraj complains that it is corrupted.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Campbell, Patrick
Sent: Thursday, May 29, 2008 11:12 AM
To: amber_at_scripps.edu
Subject: AMBER: VMD Movie 3

 

Hello Dr. Simmerling,

 

 

The ntwx value was 5000 and the nstlim value was 5000000. The job did run to
completion ie, the nstlim value was reached. I have included the script used
for the MD below. I welcome any suggestions as to possible solutions.

 

Thanks again and do have a great day!

Pat

 

 

 

 

 

 

nstlim=5000000,
dt=0.002,
ntx=5,
irest=1,
ntpr=500,
ntwr=5000,
ntwx=5000,
temp0=300.0,
ntt=1,
tautp=2.0,
ntb=2,
ntp=1,
ntc=2,
ntf=2,
nrespa=1,
&end

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