To,
David van der Spoel
Dear Sir,
I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a
problem.
I am giving job for 500000 steps step size 0.002ps (total 1ns) but my
job is stopped after 470000 steps. when i run this on 4 processors.
But the same job is completed on 2 processors.Why this happing i am not
able to understand.
Another thing is that job for 1500000 steps step size 0.002ps (total
3ns) is stopped after 375000 steps on 2 processors
and after 587000 steps on 4 processors, without any error message.
What could be the problem and how to solve it, please help me.
even i tried the 2 same jobs for 1000000 steps step size 0.002ps (total
2ns), one on single processor it is completed in 8 days
but the same job is stop after 550000 steps on 4 processors.
Is there any change is required in MPI coding or in .mdp files. Sir if
you need any other please let me know.
Please solve my problem, I will be highly obliged.
DvdS:
Please upgrade to a recent version. 3.2.1 is more than five years old.
With warm regards.
Shikhar
--
------------------------------------------------------------
Shikhar Gupta
Senior Research Fellow
Pharmacoinformatics Department
Block- A (Room No.- 208)
National Institute of Pharmaceutical Education & Research( NIPER )
Sec- 67, S.A.S Nagar
Mohali, Punjab (India)
Web-Site: www.niper.ac.in <http://www.niper.ac.in>
PIN- 160062
Email:[email protected]
<mailto:email%[email protected]>,[email protected]
<mailto:[email protected]>
--
------------------------------------------------------------
Shikhar Gupta
Senior Research Fellow
Pharmacoinformatics Department
Block- A (Room No.- 208)
National Institute of Pharmaceutical Education & Research( NIPER )
Sec- 67, S.A.S Nagar
Mohali, Punjab (India)
Web-Site: www.niper.ac.in <http://www.niper.ac.in>
PIN- 160062
Email:[email protected]
<mailto:email%[email protected]>,[email protected]
<mailto:[email protected]>
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
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