Hi Mark, Thanks for your reply. I will try to follow your instructions.
Thanks, Jesmin On Thu, Aug 9, 2012 at 9:06 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > 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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
