Thanks Justin.The simulation is indeed with CHARMM and the error went away when I used sigma and epsilon instead of C6 and C12. This run was for no scaling but now I can design the rest of the simulation without scaling the C12 term.
Thanks again Pooja On Mon, Nov 1, 2010 at 9:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sai Pooja wrote: > >> Hi, >> >> Restating that I was trying to scale the Protein Solvent interactions, I >> added a new section to the ffnonbonded.itp file. This is what the section >> looks like >> >> [ nonbond_params ] >> >> C OWT3 1 0.00335276 0.00000518 >> CA OWT3 1 0.00266209 0.00000411 >> CC OWT3 1 0.00266209 0.00000411 >> CD OWT3 1 0.00266209 0.00000411 >> CE1 OWT3 1 0.00285525 0.00000481 >> CE2 OWT3 1 0.00280380 0.00000473 >> CM OWT3 1 0.00365968 0.00000617 >> CP1 OWT3 1 0.00214019 0.00000506 >> CP2 OWT3 1 0.00307174 0.00000615 >> CP3 OWT3 1 0.00307174 0.00000615 >> CPA OWT3 1 0.00211808 0.00000227 >> CPB OWT3 1 0.00211808 0.00000227 >> CPH1 OWT3 1 0.00157456 0.00000169 >> CPH2 OWT3 1 0.00157456 0.00000169 >> CPM OWT3 1 0.00211808 0.00000227 >> ... and so on >> >> The C6 and C12 values were generated by using the sigma and epsilon values >> in the atomtypes section and then using Berthelot rules to get the sigma and >> epsilon for the interaction followed by conversion to C6 and C12. >> >> > Which force field are you using? If this is related to your manipulation > of CHARMM, then conversion from sigma/epsilon -> C6/C12 is not necessary. > The CHARMM force field uses sigma/epsilon (combination rule 2). > > > To test this new file, I started with a scaling factor of 1 but the >> simulation does not run after first 20 steps or so as the system explodes >> (LINCS warning). >> or this error >> Fatal error: >> 1 particles communicated to PME node 0 are more than 2/3 times the cut-off >> out of the domain decomposition cell of their charge group in dimension x. >> >> A simulation without this section runs fine. >> Where could I have gone wrong? I have checked the calculations. >> >> > Whatever you're doing is breaking the underlying physics of the force > field, most likely. Perhaps by weakening the intermolecular repulsion > (which scales with r^12), you're getting close contacts between the atoms in > the system. > > -Justin > > > Pooja >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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