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On 10/05/2011 1:04 PM, sreelakshmi ramesh wrote:
<blockquote
cite="mid:BANLkTi=MzHweYK8i1J_SSWnGvde+_YkOTQ@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
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...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=MzHweYK8i1J_SSWnGvde+_YkOTQ@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Tue, May 10, 2011 at 4:25 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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 moz-do-not-send="true"
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 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
moz-do-not-send="true"
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
moz-do-not-send="true"
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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