Dear Mark,<br> i followed the same stuff in the tutoriali created the table and tried the following command <br><b><br>grompp -f em.mdp -p tol.top -c nacl3.pdb</b><br>i got the following etrrors<br><br>Ignoring obsolete mdp entry 'title'<br>
Ignoring obsolete mdp entry 'cpp'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#<br><br>WARNING 1 [file tol.top, line 8]:<br> Too few parameters on line (source file toppush.c, line 315)<br><br><br>
WARNING 2 [file tol.top, line 9]:<br> Too few parameters on line (source file toppush.c, line 315)<br><br><br>ERROR 1 [file tol.top, line 13]:<br> Invalid directive nonbond params<br><br><br>WARNING 3 [file tol.top, line 15]:<br>
Too few parameters on line (source file toppush.c, line 315)<br><br><br><br><br><br><div class="gmail_quote">On Tue, May 10, 2011 at 4:25 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 10/05/2011 2:20 AM, sreelakshmi ramesh wrote:
<blockquote type="cite">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<br>
<br>
em.mdp<br>
title = nacl<br>
cpp = /usr/bin/cpp ; the c preprocessor<br>
define= -DEFLEXIBLE<br>
integrator = md<br>
dt = 0.001 ; ps !<br>
nsteps = 60000<br>
nstlist = -1<br>
ns_type = grid<br>
rlist = 1.4<br>
coulombtype = user<br>
rcoulomb = 1.0<br>
energygrps = Na Cl Sol<br>
energygrp_table = Na Cl Na Sol Cl Sol<br>
</blockquote>
<br></div>
If your mdrun -table file will be for LJ, then the only tables you
need to specify here are for Na-Cl interactions.<div class="im"><br>
<br>
<blockquote type="cite">
rvdw = 1.0<br>
vdwtype= user<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
pbc=xyz;<br>
; Energy minimizing stuff<br>
emtol = 1000.0<br>
emstep = 0.01<br>
<br>
<br>
<b>and topology file is as follows</b><br>
[ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
1 1 yes 0.5 0.8333<br>
<br>
<br>
[ atomtypes ]<br>
; name bond type mass charge ptype C A<br>
Na Na 22.99 1 A 1.0e-03<br>
Cl Cl 35.453 -1 A 9.0e-06<br>
<br>
<br>
<br>
[ nonbond params ]<br>
;i j func A B C<br>
Na Cl 1 2.01E-09 3.154 11.2E-12 (buckingham)<br>
<br>
I dont have idea how to include water topology and include A B
paramaters for water-ion interaction (lennard jones)<br>
</blockquote>
<br></div>
Set up a normal aqueous Na Cl simulation and adapt that. Consult
tutorial material for examples for including water.<br>
<br>
See <a href="http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials" target="_blank">http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials</a>,
like I suggested you search for earlier...<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<br>
<br>
any help appreciated,<br>
sree lakshmi<br>
<br>
<div class="gmail_quote">On Mon, May 9, 2011 at 12:37 PM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div> On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote:
<blockquote type="cite">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...</blockquote>
<br>
</div>
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.
<div><br>
<br>
<blockquote type="cite">i wanted some information on how
to use these tables for starting thee simulation <br>
</blockquote>
<br>
</div>
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.<br>
<font color="#888888"> <br>
Mark</font>
<div><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">On Mon, May 9, 2011 at 11:20
AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex; margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204, 204, 204);">
<div>On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex; margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204, 204, 204);">dear gmx users,<br>
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...<br>
</blockquote>
<br>
</div>
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.<br>
<br>
Mark<br>
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