David, What should not be working in the current version? Do you mean that any polarizable model (water for example) can run on a single processor only? I am currently using the model by Roux et al. for NaCl solution in SWM4-NDP model and everything seems to be working fine. I also had some problems with the collapsing of the system which seems to be solved by setting explicitly all pair interactions in [nonbond_param] statement (I had a feeling that mixing rule did not work for some reason). The results are very reasonable. Does it mean that I am doing something completely wrong?
Many thanks in advance, Mikhail On 2011-03-01 22.06, Abhijeet Joshi wrote: > Hi all, > > I am trying implement polarizable model for halides > suggested by Roux group. > I am not able to equilibrate such system. In present gromacs versions this runs on 1 processor (core) only. > > System: Sodium Iodide in water > I am using following topology file for iodide. > > Anybody has any clue what might be happening? > > Question 2: I am having trouble finding implementation details for > thole_polarization. > How would that appear in topology file? > > > > ; > ; Topology file for iodide polarizable > > [ moleculetype ] > ; molname nrexcl > I 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > 1 II 1 SI CI1 1 3.733085 > 2 IS 1 SI SI 1 -4.733085 > > > [ polarization ] > ; See notes above. alpha (nm^3) > 1 2 1 0.007439 > > > > [ exclusions ] > ; iatom excluded from interaction with i > 1 2 > 2 1 > > #ifdef POSRES > ; Restrain the oxygen... > [ position_restraints ] > ; iatom type fx fy fz > 1 1 100 100 100 > #endif > > > > Your help will be greatly appreciated > > Thanks > ~ Abhijeet > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. [email protected] http://folding.bmc.uu.se -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
