[gmx-users] regarding nacl simulation in water using tabulated potentials
sree.lakshmi at research.iiit.ac.in
Mon May 9 18:20:34 CEST 2011
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
title = nacl
cpp = /usr/bin/cpp ; the c preprocessor
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
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
; 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,
On Mon, May 9, 2011 at 12:37 PM, Mark Abraham <Mark.Abraham at 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
> 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
> 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.
> On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <Mark.Abraham at 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.
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