On 10/08/2012 3:06 AM, jesmin jahan wrote:
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?
It's a side-effect of the "Force" component of the timing breakdown.
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?
No, but if you run yourself out of memory results are unpredictable.
Consult your .log and stdout files for clues what is going on.
3. Can I only calculate the GB-polarization energy without calculating
any Forces? How?
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
4. What are the good tools to get the GB- energy values along with the
time to calculate the GB-energy?
As above.
Mark
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