[gmx-users] regarding nacl simulation in water using tabulated potentials
Mark.Abraham at anu.edu.au
Tue May 10 00:55:09 CEST 2011
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
> 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
> ; 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.
like I suggested you search for earlier...
> 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.
>> 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
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users