You haven't really described anything about your system, so something else
certainly could be at play here.
ntt=2 is identical to ntt=0 (the default) for short simulations (unless you
explicitly set vrand to be a very small number compared to nstlim, I don't
know what the default is). However, if your simulation is that unstable in
so few steps, there are probably more issues than a thermostat can fix (in
any event ntt=1 or 3 with appropriate options could potentially be a better
choice). Have you optimized the system? It looks like you are switching
from HF/3-21G to PBE/6-31G, I wouldn't be terribly surprised if the
geometries are appreciably different.
I think we would need more information to diagnose the problem. I'm
assuming sander bombs due to a vlimit error? Otherwise there isn't
necessarily a reason why you couldn't continue with the simulation in
principle.
Regards,
Brian
On Tue, May 8, 2012 at 1:35 PM, <c00jsw00.nchc.narl.org.tw> wrote:
> Dear Sir,
> I have used the thermostat method (ntt=2). But the system temperature is
> up to ~700 K. I also used the g09 instead of
> Terachem and g09 work fine (T~=300 K).
> YT
>
> -----Original message-----
> From:Brian Radak <radak004.umn.edu>
> To:AMBER Mailing List <amber.ambermd.org>
> Date:Tue, 08 May 2012 20:32:07
> Subject:Re: [AMBER] About the system temperature of QMMM simulations
> (amber12+ Terachem V1.5 )
>
> You didn't set an initial temperature (tempi) in your input file. The
> instantaneous temperature probably rose very quickly due to large forces.
> A thermostat would likely be useful if your starting configuration is not
> of a high Boltzmann weight (ntt, temp0, + other options). I would
> recommend checking out the relevant sections in the AMBER12 manual.
>
> Regards,
> Brian
>
> On Mon, May 7, 2012 at 9:05 PM, Yeng-Tseng Wang <c00jsw00.gmail.com>
> wrote:
>
> > Dear all,
> > 1. My computer setting is : CPU: AMD Phenom X 6 and GPU: GTX 580 (1.5G)
> > 2. I modified the test case (amber12/test/qmmm_EXTERN/ QMMM_MD_TeraChem/
> > Run.nma-spcfw-15.hf_sto-3g) and used the PBE method/ 6-31 basis to
> simulate
> > the case. After 16 steps, the system temperature raise too high(~6000K).
> > Could you tell me how to fix the problem?
> >
> > Thank you
> > YT
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
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> radakb.biomaps.rutgers.edu
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> Sorry for the multiple e-mail addresses, just use the institute appropriate
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue May 08 2012 - 11:30:02 PDT
