<br><br>Thanks Justin.The simulation is indeed with CHARMM and the error went away when I used sigma and epsilon instead of C6 and C12. This run was for no scaling but now I can design the rest of the simulation without scaling the C12 term.<br>
<br>Thanks again<br>Pooja<br><br><div class="gmail_quote">On Mon, Nov 1, 2010 at 9:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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><br>
<br>
Sai Pooja 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,<br>
<br>
Restating that I was trying to scale the Protein Solvent interactions, I added a new section to the ffnonbonded.itp file. This is what the section looks like<br>
<br>
[ nonbond_params ]<br>
<br>
C OWT3 1 0.00335276 0.00000518<br>
CA OWT3 1 0.00266209 0.00000411<br>
CC OWT3 1 0.00266209 0.00000411<br>
CD OWT3 1 0.00266209 0.00000411<br>
CE1 OWT3 1 0.00285525 0.00000481<br>
CE2 OWT3 1 0.00280380 0.00000473<br>
CM OWT3 1 0.00365968 0.00000617<br>
CP1 OWT3 1 0.00214019 0.00000506<br>
CP2 OWT3 1 0.00307174 0.00000615<br>
CP3 OWT3 1 0.00307174 0.00000615<br>
CPA OWT3 1 0.00211808 0.00000227<br>
CPB OWT3 1 0.00211808 0.00000227<br>
CPH1 OWT3 1 0.00157456 0.00000169<br>
CPH2 OWT3 1 0.00157456 0.00000169<br>
CPM OWT3 1 0.00211808 0.00000227<br>
... and so on<br>
<br>
The C6 and C12 values were generated by using the sigma and epsilon values in the atomtypes section and then using Berthelot rules to get the sigma and epsilon for the interaction followed by conversion to C6 and C12.<br>
<br>
</blockquote>
<br></div>
Which force field are you using? If this is related to your manipulation of CHARMM, then conversion from sigma/epsilon -> C6/C12 is not necessary. The CHARMM force field uses sigma/epsilon (combination rule 2).<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
To test this new file, I started with a scaling factor of 1 but the simulation does not run after first 20 steps or so as the system explodes (LINCS warning).<br>
or this error<br>
Fatal error:<br>
1 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.<br>
<br>
A simulation without this section runs fine.<br>
Where could I have gone wrong? I have checked the calculations.<br>
<br>
</blockquote>
<br></div>
Whatever you're doing is breaking the underlying physics of the force field, most likely. Perhaps by weakening the intermolecular repulsion (which scales with r^12), you're getting close contacts between the atoms in the system.<br>
<br>
-Justin<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Pooja<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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