[gmx-users] regarding nacl simulation in water using tabulated potentials

[sreelakshmi ramesh]

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.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
> 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.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.
>>
>> Mark
>> --
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>
>
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