AMBER Archive (2009)

Subject: RE: [AMBER] Sander Stalling

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 06 2009 - 11:58:58 CDT

Hi Steve,

This may be too big for AMBER 8 - I'm not sure. However I suspect you have
ntb set wrong. Often if you set ntb=1 (the default) but give it a gas phase
inpcrd file it can hang - try adjusting ntb.

Also try setting ntpr=1. Perhaps, if this is a restart, it is running but
running extremely slowly so it doesn't reach the number of steps for a
print.

For something this big you should probably consider AMBER 10 with PMEMD, it
will run significantly faster.

All the best
Ross

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of Steve Seibold
Sent: Monday, April 06, 2009 9:22 AM
To: amber_at_ambermd.org
Subject: [AMBER] Sander Stalling

Hello AMBER

 

I have installed AMBER 8 on a new system. When I run sander the output
prints out to where it list the SIZE OF NONBOND LIST. At this point, I
can wait for an hour and nothing happens although sander is still
running. My worry is that my protein system with waters may be too
large. I have over 200,000 atoms with 54169900 nonbonded contacts. Would
a stalling at this point in the log be symptomatic of too large a
system? If so, I can compile AMBER to accept larger systems?

 

Thanks,

Steve

 

 

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