From: amin_at_imtech.res.in
Date: Wed Jun 27 2012 - 01:34:28 CDT
Thanks. I am heating the system from 0k to 300k in 3000 steps. I checked the
structure but couldn't find something obviously wrong.I will check again.I am
attaching my config file. Can you please check for some problems in it? Regards.
Amin.
> I'm not sure you necessarily did anything wrong. I would suggest that your
system even after 50,000 steps still has some kind of problems, but the CPU
integrator is robust enough to muscle through it, whereas the CUDA one is not.
>
> You should consider slowly heating your system from say 100K or something of
the sort, as I would imagine you have jumped straight to 300K which generally
works, but requires a decent starting point.
>
> Keep in mind that even though the minimizer in NAMD is smarter than just
steepest descent, it will still be easily trapped in local minima, so doing
more minimization without some kind of dynamics is unlikely to get you closer
to the global minimum and away from whatever problems you have.
>
> Did you have a look at the structure also, and which atoms are causing the
problem?
>
> ~Aron
>
> On Wed, Jun 27, 2012 at 1:37 AM, <amin_at_imtech.res.in> wrote:
>
>> Dear all,
>> I am trying to run an equilibration using NAMD 2.9-CUDA on Linux.
>> However,
>> I keep getting "Atoms moving too fast error".I increased the minimization
upto 50000 steps but it doesn't work. But when I tried to run the exact same
config file using the non-CUDA version it ran without any error even at 10000
minimization steps.And the error is reproducible. Can someone please tell me
what may have gone wrong.
>> Regards.
>> Amin.
>> ______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute
of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए,
चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036
>> दूरभाष/EPABX :0172 6665 201-202
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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