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

[Mark Abraham]

On 10/05/2011 2:20 AM, sreelakshmi ramesh wrote:
> 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

If your mdrun -table file will be for LJ, then the only tables you need 
to specify here are for Na-Cl interactions.

> 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)

Set up a normal aqueous Na Cl simulation and adapt that. Consult 
tutorial material for examples for including water.

See http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials, 
like I suggested you search for earlier...

Mark

>
>
> any help appreciated,
> sree lakshmi
>
> On Mon, May 9, 2011 at 12:37 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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 <mailto: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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