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>
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>
<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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