Re: Questions concerning NAMD

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Sep 09 2008 - 15:07:22 CDT

Hi Michalis,

mxenos_at_notes.cc.sunysb.edu wrote:
>
>
>
> 1. We cannot apply a small force at each particle. It seems that
> the smallest force that we can apply is in the order of magnitude
> 0.001 kcal/mole/A. Our calculations indicate that we need a much
> smaller force, e.g. 10^-10 N. Could you please comment on this ?
>
You might want to try using the constantForceScaling command to further
scale your forces; this, unlike the forces present in the pdb file used
to set up constantforces, should not be restricted to the field width of
the pdb.
>
>
>
> 2. We solve the problem under consideration in a powerful
> parallel computer, BlueGene/L. Though, it seems that NAMD can handle
> only one milion particles on BG/L. Could you comment on this ? Is this
> a limitation of NAMD? Do you have any idea how we can overcome this
> problem?
>
>
>
What problem are you running into? If you're getting crashes on startup,
try using the memory optimized version of namd
(http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction)
and follow the other guidelines on that page for reducing memory usage.
The BlueGene/L architecture has many fine qualities, but it does not
have much memory per node, which can lead to problems.
>
> 3. Could you guide us through some papers for the temperature
> definition in NAMD? Is the temperature in NAMD defined as the sum of
> internal energy, e.g. c_p T and kinetic energy, m u^2 ?
>
The instantaneous temperature in namd is simply calculated from the
kinetic energy ( sum(1/2 m v^2)) using the equipartition relation.

Hope this is helpful.
Best,
Peter
>
>
>
> We thank you very much for your help and we are looking forward to
> your response.
>
>
>
> Best regards,
>
> Michalis
> -----------------------------------------------------
> Michalis Xenos, PhD
> Postdoctoral Research Associate
> Bio-Fluids Laboratory
> Stony Brook University, Stony Brook, NY
>
> phone: 631-444-2799
> email: mxenos_at_notes.cc.sunysb.edu <mailto:mxenos_at_notes.cc.sunysb.edu>

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