2015-11-16 6:32 GMT-07:00 Rom <[email protected]>: > > > On Thursday, 12 November 2015 18:28:25 UTC, Christoph Junghans wrote: >> >> 2015-11-12 5:51 GMT-07:00 Rom <[email protected]>: >> > 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!) I don't really have a good idea right now, did you try the original example to check if that works?
Christoph > > > > > > >> >> 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]. >> > 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. >> >> >> >> -- >> 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. -- 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.
