[gmx-users] About getting running time from a Gromacs Run

jesmin jahan shraban03 at gmail.com
Thu Aug 9 19:06:00 CEST 2012

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.


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?


Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.

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