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.abra...@anu.edu.au
<mailto: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 <mailto: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
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