On Thursday, 12 November 2015 18:28:25 UTC, Christoph Junghans wrote: > > 2015-11-12 5:51 GMT-07:00 Rom <[email protected] <javascript:>>: > > Hello all! > > > > I have a small query, and I couldn't find it anywhere else on this page. > > > > I'm doing hybrid FM of hexane (256 molecules in a box), where boltzmann > > inversion for the bonded, and FM for the non-bonded. > > My simulation appeared to show all of my hexane molecules clumping > together > > (literally a giant ball of dense hexanes). > > > > I compared my non bonded potential e.g. A-A, to the potential given in > the > > paper: > > > > Victor Ruehle, Christoph Junghans, Macrolmol. Theory Simul. 2011, 20, > > 472-477 (Hybrid approaches to coarse-graining using the VOTCA package: > > Liquid Hexane) > > > > I have an attractive well depth of -20kj/mol (attached, plot column 1 > and > > 6), whereas the potential in the paper has a well depth of -1 kj/mol, so > > mine is far too attractive (which explains the extreme aggregation)! > Even my > > slight repulsive bump at the zero line is almost 0.8 kj/mol. > > > > Is there any obvious reason why my potential could be this off? Is it an > > effect of maybe how I choose my grid size, or blocking averages when > force > > matching? > Did you follow the hexane/hybrid_force_matching tutorial? > < > https://github.com/votca/csg-tutorials/tree/master/hexane/hybrid_force_matching> > > > > Grid size, or blocking averages when force matching only matter if you > running low on statistics. > I seems to me, you might have forgot to the rerun step using mdrun to > subtract the force. > > Hi Christoph! Thank you for the reply! OK, so its not grid size or blocking averages (I am using around 5000 force outputs). Yes! I've been using the hexane tutorial as my base, looking at all the scripts etc. And I did output the individual force interactions using -rerun (by using energygrp_excl in the mdp file (attached)), and running the following gromacs command.
grompp_mpi -f md_AA.mdp -c heat0_npt10.gro -p topol.top -n index.ndx -o npt_prod_AA.tpr -maxwarn 1 mpirun -n $SLURM_NTASKS mdrun_mpi -rerun npt_production.trr -v -deffnm npt_prod_AA [where md_AA.mdp is the specific mdp file for my AA interaction, heat0_npt10.gro is my original .gro file, and npt_production.trr is the original trajectory file which includes all the interactions, which I am now trying to only specify for AA interactions using -rerun} Can you see any obvious mistake, since its such a simple system, I'm struggling to see what the issue is? (Also, I'm unsure if this is a gromacs issue, or a VOTCA issue, so I apologise!) > Christoph > > > > > If you need anymore files or details, please just let me know, I will be > > happy to provide them! and thank you for all the help :D > > > > Many thanks > > Rom > > > > > > > > -- > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
md_AA.mdp
Description: Binary data
