AMBER Archive (2007)

Subject: Re: AMBER: Box problems in vacuum minimization with sander.serial 8

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 13 2007 - 13:34:57 CST

On Tue, Feb 13, 2007, j j wrote:

> I'm trying to carry out a very simple minimization.
> For this purpose I'm using the following flags:
> Minimization
> &cntrl
> imin=1, ntr=0,
> cut=6, ntpr=100, scee=1.2, drms=0.0001,
> maxcyc= 3000, ntmin=1, ncyc=1000, nsnb=25,
> dielc = 4.0,
> &end
> After getting the topology and coord file from xleap,
> I try to launch sander8.serial and I got the following errors:
> a) If I do not set a box sander start running but do not
> print any result while one processor is at 100%.

If you have no box, you need to set ntb=0 in your input file (since
ntb=1 is the default). I'm not sure why the process hangs: it should
print an error message.

> b) If I set a box:
> setbox NSER centers

You don't want to do this for a vacuum simulation.

...hope this helps...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu