On 10/05/2011 1:04 PM, sreelakshmi ramesh wrote:
Dear Mark,
i followed the same stuff in the tutoriali created
the table and tried the following command
*
grompp -f em.mdp -p tol.top -c nacl3.pdb*
i got the following etrrors
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
WARNING 1 [file tol.top, line 8]:
Too few parameters on line (source file toppush.c, line 315)
WARNING 2 [file tol.top, line 9]:
Too few parameters on line (source file toppush.c, line 315)
ERROR 1 [file tol.top, line 13]:
Invalid directive nonbond params
WARNING 3 [file tol.top, line 15]:
Too few parameters on line (source file toppush.c, line 315)
So either you're wrong or the tutorial's wrong. How can anybody here
tell? Only you can look at the lines of tol.top and see why grompp
doesn't like them...
Mark
On Tue, May 10, 2011 at 4:25 AM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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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