Dear Gromacs Users,
I am a new user of Gromacs and I am using gromacs to calculate
GB-polarization energy .
I have a couple of questions about it. It would be great if someone
can answer them. Thanks in advance.
Questions:
1: I got an output like this in log file from a protein simulation:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Comm. coord. 24 1 0.235 0.1 1.0
Force 24 1 17.369 5.2 71.9
Wait + Comm. F 24 1 0.258 0.1 1.1
Write traj. 24 1 0.296 0.1 1.2
Update 24 1 0.005 0.0 0.0
Comm. energies 24 2 7.252 2.2 30.0
-----------------------------------------------------------------------
Total 24 24.157 7.3 100.0
-----------------------------------------------------------------------
NOTE: 30 % of the run time was spent communicating energies,
you might want to use the -gcom option of mdrun
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 0.303 0.303 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 54.029 0.285 84.257
Now my question is: What is the time to calculate the GB-polarization
Energy that is shown in log? Or How to get the time?
2. I have a protein with 1.5 million atoms. I tried to run it with
gromacs on 16 machines each with 12 cores. It generated a segmentation
fault. Is there any size limit to run in gromacs?
3. Can I only calculate the GB-polarization energy without calculating
any Forces? How?
4. What are the good tools to get the GB- energy values along with the
time to calculate the GB-energy?
Thanks,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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