i had three tables one for solvent na and solvent cl ions (obeying lj potential) and na ,cl obeying my own potential.i have the following mdp file
em.mdp title = nacl cpp = /usr/bin/cpp ; the c preprocessor define= -DEFLEXIBLE integrator = md dt = 0.001 ; ps ! nsteps = 60000 nstlist = -1 ns_type = grid rlist = 1.4 coulombtype = user rcoulomb = 1.0 energygrps = Na Cl Sol energygrp_table = Na Cl Na Sol Cl Sol rvdw = 1.0 vdwtype= user fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 pbc=xyz; ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 *and topology file is as follows* [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.5 0.8333 [ atomtypes ] ; name bond type mass charge ptype C A Na Na 22.99 1 A 1.0e-03 Cl Cl 35.453 -1 A 9.0e-06 [ nonbond params ] ;i j func A B C Na Cl 1 2.01E-09 3.154 11.2E-12 (buckingham) I dont have idea how to include water topology and include A B paramaters for water-ion interaction (lennard jones) any help appreciated, sree lakshmi On Mon, May 9, 2011 at 12:37 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote: > > i had followed the instructions in themnaual for ninbonded interactions adn > had created two tables one for nacl adn other table for water ion > interations... > > > That's not "I really don't have any idea on how to do this". Please ask > the question you want answered, or you're wasting everyone's time. > > > i wanted some information on how to use these tables for starting thee > simulation > > > Sorry, that's too general. You might want help with a command line, or > setting up the .mdp, or something else. Please read 6.7 of the manual, try > things, and ask a focused question. > > Mark > > > On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: >> >>> dear gmx users, >>> i have to simulate nacl in water...the system is >>> acubic box with just one na adn one cl ion in tip3p water.i wanted to use a >>> buckingham potential for na adn cl interaction and lennard jones for water >>> -ion intercation.i really dont have any idea on how to do this.any help will >>> be of great use for me... >>> >> >> Can't be done simply. You'd have to use non-bonded interaction tables for >> the Na-Cl interaction with properly constructed energy groups. Search the >> manual and webpage for details. >> >> Mark >> -- >> 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 >> > > > > -- > 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 >
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