[gmx-users] Problem with PME

[Srikrishna Sureshkumar]

Dear All

I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation runs for
ever. No output is generated it appears like the system is being put in the
leep mode.

I am ataching my MDP file. I would like to know if there is any correction I
could do so that i can do my simulation properly. At the same time if I use
coloubtype cut-off instaed of PME the simulation goes on properly and the
only problem is that it does not converge in a single run.

Thanks and Regards

S. Srikrishna
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[David van der Spoel]

Post by Srikrishna Sureshkumar
Dear All
I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation runs
for ever. No output is generated it appears like the system is being put
in the leep mode.

Are you running this on SGI?

I'm not sure what it could be, the mdp file is fine.

Post by Srikrishna Sureshkumar
I am ataching my MDP file. I would like to know if there is any
correction I could do so that i can do my simulation properly. At the
same time if I use coloubtype cut-off instaed of PME the simulation goes
on properly and the only problem is that it does not converge in a
single run.
Thanks and Regards
S. Srikrishna
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[Srikrishna Sureshkumar]

Dear David,

No, I am runing this on a Intel P3 System with redhat 7.2.

Regards
Srikrishna
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[David van der Spoel]

Post by Srikrishna Sureshkumar
Dear David,
No, I am runing this on a Intel P3 System with redhat 7.2.

And did you compile gromacs and fftw yourself?

Post by Srikrishna Sureshkumar
Regards
Srikrishna
------------------------------------------------------------------------
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[S. Srikrishna]

Dear David

Post by David van der Spoel
And did you compile gromacs and fftw yourself?

No. System admisitrator did that. If it is a installation problem even with
coloumbtype "cut-off" it shouldnt work.
And PME works some times with integrator "md".

Regards
Srikrishna

[David van der Spoel]

Post by Srikrishna Sureshkumar
Dear David

Post by David van der Spoel
And did you compile gromacs and fftw yourself?

No. System admisitrator did that. If it is a installation problem even
with coloumbtype "cut-off" it shouldnt work.
And PME works some times with integrator "md".

Sometimes there can be problems with multiple installed FFTW libraries,
i.e. you link against one library and use another.

It is difficult to debug, but the installation is the first suspect. If
you say it sometimes works, does it work reproducibly? If not you might
have a hardware problem.

Post by Srikrishna Sureshkumar
Regards
Srikrishna
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[Daniela S. Mueller]

hi s.,

as you are using the integrator steep, i assume you are running energy
minimisations?
in that case i suspect that the type of coulomb-interaction model is not
critical, so you can set it to cut-off.
what i have found is that energy minimisation doesn't work with
coulomb-type = (generalised) reaction-field, so it might be the same
case with pme.

@david van der spoel: is this a bug?

best regards and good luck,
daniela

Post by Srikrishna Sureshkumar
Dear All
I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation
runs for ever. No output is generated it appears like the system is
being put in the leep mode.
I am ataching my MDP file. I would like to know if there is any
correction I could do so that i can do my simulation properly. At the
same time if I use coloubtype cut-off instaed of PME the simulation
goes on properly and the only problem is that it does not converge in
a single run.
Thanks and Regards
S. Srikrishna

--
Daniela S. Mueller

biologist (Diplom, German degree)
______________________________________________________________________

- Molecular Dynamics Group, UQ -

Address:
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane
Australia

Phone: [phone]

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm

**********************************************************************

- MD group, RuG -

Address:
Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Website: http://www.rug.nl/gbb/md
______________________________________________________________________

[David Mobley]

Minimization generally works fine for me with PME, so I would suspect
either the system topology/coordinates or the GROMACS installation,
rather than a bug. I do steepest descents minimization with PME all
the time.

David

Post by Daniela S. Mueller
hi s.,
as you are using the integrator steep, i assume you are running energy
minimisations?
in that case i suspect that the type of coulomb-interaction model is not
critical, so you can set it to cut-off.
what i have found is that energy minimisation doesn't work with
coulomb-type = (generalised) reaction-field, so it might be the same
case with pme.
@david van der spoel: is this a bug?
best regards and good luck,
daniela

Post by Srikrishna Sureshkumar
Dear All
I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation
runs for ever. No output is generated it appears like the system is
being put in the leep mode.
I am ataching my MDP file. I would like to know if there is any
correction I could do so that i can do my simulation properly. At the
same time if I use coloubtype cut-off instaed of PME the simulation
goes on properly and the only problem is that it does not converge in
a single run.
Thanks and Regards
S. Srikrishna

--
Daniela S. Mueller
biologist (Diplom, German degree)
______________________________________________________________________
- Molecular Dynamics Group, UQ -
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane
Australia
Phone: [phone]
Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm
**********************************************************************
- MD group, RuG -
Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Website: http://www.rug.nl/gbb/md
______________________________________________________________________
_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
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