On Thu, Oct 7, 2021 at 9:48 AM Satyen Dhamankar <[email protected]> wrote: > > Thank you for your response Christoph! > > I also have a quick question about performance. > > These simulations consisting of about 11000 atoms (not a very large system), > is taking much longer than my all-atom simulation. I am seeing the following > message in when mdrun is run on GMX: > > "Multiple energy groups is not implemented for GPUs, falling back to the CPU. > For better performance, run on the GPU without energy groups and then do gmx > mdrun -rerun option of the trajectory with an energy group .tpr file." > > Is the lack of GPU support leading to about 0.1 ns/hr speeds? Are tabulated > potentials for non-bonded/bonded interactions slower in GMX? If you have a GPU in your machine that is correct. There is not much we on the VOTCA side can do here, but wait. Please free to ping the gromacs developers for a status update here: https://gitlab.com/gromacs/gromacs/-/issues/1347
Christoph > > On Wednesday, October 6, 2021 at 12:14:25 PM UTC-4 Christoph Junghans wrote: >> >> On Wed, Oct 6, 2021 at 9:04 AM Satyen Dhamankar <[email protected]> wrote: >> > >> > Hello, >> > >> > I am running IBI on a particular polymer simulation, and I VOTCA has some >> > files in step_xxx directories. My question is, given a distribution I have >> > asked to recreate, A-B.dist.tgt, how do I check the extent to which it has >> > been reproduced in the simulation? >> >> dist.new is the file to check, it is the distribution done with the >> current potential. (.pot.cur) >> >> > For example, I am trying to optimize TW-TW.dist.tgt, and these are all the >> > TW-TW files that have been generated: >> > >> > TW-TW.conv >> > TW-TW.dist.conv >> > TW-TW.dist.new >> > TW-TW.dist.new.resample.fnF >> > TW-TW.dist.tgt >> > TW-TW.dist.tgt_extrapolated.hpVpl >> > TW-TW.dist.tgt_extrapolated_left.fLt6f >> > TW-TW.dist.tgt_extrapolated_left.RchsI >> > TW-TW.dist.tgt_extrapolated.ly2nG >> > TW-TW.dist.tgt_smooth.TEwdo >> > TW-TW.dist.tgt_smooth.TiJo0 >> > TW-TW.dpot.1 >> > TW-TW.dpot.new >> > TW-TW.dpot.pure_ibi >> > TW-TW.pot.1 >> > TW-TW.pot.2 >> > TW-TW.pot.3 >> > TW-TW.pot.cur >> > TW-TW.pot.extrapol.8Lku6 >> > TW-TW.pot.interpol.P4rlN >> > TW-TW.pot.new >> > TW-TW.pot.shift.QoRc9 >> > TW-TW.pot.smooth.hnK0t >> > TW-TW.pot.smooth.hnK0t.onlyleft.zhxPa >> > >> > Furthermore, in the event that IBI has converged successfully, are the >> > tables, table_TW_TW.xvg what I am supposed to use for a long-scale >> > simulation? >> Correct! >> >> > >> > Jumping off of the question above, if I want to run an IBI where I want to >> > recreate other potentials and use the potentials developed by a previous >> > IBI. For example, running an IBI on bonded potentials after running an IBI >> > on non-bonded potentials, how do I do this on VOTCA? >> >> If you want to iterate on them more, you can put a <name>.pot.in in >> the main directory as an initial guess. >> If you don't want to iterate on them more, you just add the final xvg >> file to <filelist> and remove their block from settings.xml. >> >> Christoph >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/8c4cfe4b-9ab3-44d3-8cc7-9c3afe031720n%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/a5d36399-0df3-40f8-9741-7f12e958fdc2n%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e6FtHbiuR_XoozOgHETVnH3a_vq-EQ3vV91_zWtuN9WDg%40mail.gmail.com.
