Dear Brian,
After upgrading Terachem (1.5beta=>1.5) , I have fixed the problem.
Thanks for your suggestions.
YT
2012/5/9 Brian Radak <radak004.umn.edu>
> 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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> >
> >
> > --
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> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
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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
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> Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Wed May 16 2012 - 02:00:02 PDT
