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

From: j j <fantvamp.gmail.com>
Date: Tue, 13 Feb 2007 20:43:34 +0100

Thank you very much,
I forgot set ntb=0 for
no periodicity is applied and PME off.
I've set the nonbonded cutoff of 12 ,
and work fine.
Thanks again.
Best Regards,
JJ

2007/2/13, David A. Case <case.scripps.edu>:
>
> 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
>
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Received on Wed Feb 14 2007 - 06:07:44 PST
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