Oh ohk, <br>I have been running in parallel<br><br>Thanks David,<br>
<br><div class="gmail_quote">On Tue, Mar 1, 2011 at 3:12 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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 class="im">On 2011-03-01 22.06, Abhijeet Joshi wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi all,<br>
<br>
I am trying implement polarizable model for halides<br>
suggested by Roux group.<br>
I am not able to equilibrate such system.<br>
</blockquote>
<br></div>
In present gromacs versions this runs on 1 processor (core) only.<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
System: Sodium Iodide in water<br>
I am using following topology file for iodide.<br>
<br>
Anybody has any clue what might be happening?<br>
<br>
Question 2: I am having trouble finding implementation details for<br>
thole_polarization.<br>
How would that appear in topology file?<br>
<br>
<br>
<br>
;<br>
; Topology file for iodide polarizable<br>
<br>
[ moleculetype ]<br>
; molname nrexcl<br>
I 1<br>
<br>
[ atoms ]<br>
; id at type res nr residu name at name cg nr charge<br>
1 II 1 SI CI1 1 3.733085<br>
2 IS 1 SI SI 1 -4.733085<br>
<br>
<br>
[ polarization ]<br>
; See notes above. alpha (nm^3)<br>
1 2 1 0.007439<br>
<br>
<br>
<br>
[ exclusions ]<br>
; iatom excluded from interaction with i<br>
1 2<br>
2 1<br>
<br>
#ifdef POSRES<br>
; Restrain the oxygen...<br>
[ position_restraints ]<br>
; iatom type fx fy fz<br>
1 1 100 100 100<br>
#endif<br>
<br>
<br>
<br>
Your help will be greatly appreciated<br>
<br>
Thanks<br>
~ Abhijeet<br>
<br>
</blockquote>
<br>
<br></div></div>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br><font color="#888888">
-- <br>
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</font></blockquote></div><br><br clear="all"><br>-- <br><div><div> Abhijeet Joshi
<br> Research Assistant
<br> Molecular Thermodynamics and Statistical Mechanics Research Group
<br> University of Wisconsin-Madison
<br> <a href="http://www.engr.wisc.edu/groups/mtsm/index.shtml" target="_blank">http://www.engr.wisc.edu/groups/mtsm/index.shtml</a>
<br> <a href="mailto:aajoshi2@wisc.edu" target="_blank">aajoshi2@wisc.edu</a>
<br> 608-320-9215
<br></div><div> </div></div><br>