Hi David,
When Vlimit starts exceeding, simulation stops after something and gives me
this error
vlimit exceeded for step 117254; vmax = 214.9892
vlimit exceeded for step 117255; vmax = 27.5224
vlimit exceeded for step 117256; vmax = 161.4443
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
How to solve this problem?
Thanks
Piyush
On Mon, Aug 25, 2008 at 2:52 PM, Piyush Wanjari <ppwanjari.gmail.com> wrote:
> Hi David,
>
> Thanks for reply. Yes, I tried running using just one processor and problem
> of inhomogeneous system stopped.
> for ntt=3, what value of gamma_ln and for ntt=2 what value of vrand should
> be used?
>
> Thanks
>
> Piyush
>
> On Fri, Aug 22, 2008 at 10:11 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
>
>> On Wed, Aug 20, 2008, Piyush Wanjari wrote:
>> >
>> >
>> > | Local SIZE OF NONBOND LIST = 41794
>> > | TOTAL SIZE OF NONBOND LIST = 559211
>> > ***** Processor 0
>> > ***** System must be very inhomogeneous.
>>
>> You can try running the equilibration on just one cpu to see if that
>> changes things. You might see visually if your system appears to be
>> inhomogeneous.
>>
>> > inp2
>> >
>> > &cntrl
>> > imin=0, ntx=1, irest=0, ntpr=100, ntwr=1000, ntwx=100,
>> > ntwe=500, ntf=2, ntb=1, nstlim=100000,
>> > temp0 = 300.0, tempi=300.0, ntt=2, tautp=1.0,
>> ^^^^^^^
>>
>> Setting ntt=2 without setting vrand is probably dangerous. I would
>> suggest ntt=3 for equilibration. But it's not clear that this is
>> related to your problem or not.
>>
>> What happens after the vlimit messages? It could be that you have a
>> very weird stating configuration, and that a run with real temperature
>> equilibration would help.
>>
>> ...good luck...dac
>>
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>
>
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Received on Wed Aug 27 2008 - 06:07:34 PDT
