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? 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.
