Oh ohk, I have been running in parallel Thanks David,
On Tue, Mar 1, 2011 at 3:12 PM, David van der Spoel <[email protected]>wrote: > 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 > -- Abhijeet Joshi Research Assistant Molecular Thermodynamics and Statistical Mechanics Research Group University of Wisconsin-Madison http://www.engr.wisc.edu/groups/mtsm/index.shtml [email protected] 608-320-9215
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