Following is the mdp file<div><br></div><div><div>cpp = /usr/bin/cpp</div><div>;define = -DFLEX_SPC</div><div>constraints = none</div><div>integrator = steep</div><div>nsteps = 10000</div>
<div>;</div><div>; Energy minimizing stuff</div><div>;</div><div>emtol = 200</div><div>emstep = 0.01</div><div>pbc = no</div><div>nstcomm = 0</div><div>ns_type = grid</div>
<div>coulombtype = Cut-off </div><div>rlist = 60</div><div>rcoulomb = 60</div><div>rvdw = 60</div><div>Tcoupl = no</div><div>Pcoupl = no</div><div>
gen_vel = no</div><div><br></div><div>E_x = 1 0 0</div><div>E_y = 1 0 0</div><div>E_z = 1 0 0</div><div><br></div><div><br></div><div>Following is the energy term</div><div><br></div><div><div> Step Time Lambda</div>
<div> 0 0.00000 0.00000</div><div><br></div><div> Energies (kJ/mol)</div><div> Bond Angle LJ (SR) Coulomb (SR) Potential</div><div> 1.11496e-07 0.00000e+00 0.00000e+00 9.90561e+05 9.90561e+05</div>
<div> Pressure (bar)</div><div> 0.00000e+00</div><div><br></div><div> Step Time Lambda</div><div> 1 1.00000 0.00000</div><div><br></div><div> Energies (kJ/mol)</div>
<div> Bond Angle LJ (SR) Coulomb (SR) Potential</div><div> 7.55922e-02 0.00000e+00 0.00000e+00 9.90324e+05 9.90324e+05</div><div> Pressure (bar)</div><div> 0.00000e+00</div>
</div><div><br></div><div><br></div><div>Amit</div><br><div class="gmail_quote">On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin, when i define the whole line charge as a charge group i do get a coulomb energy contribution. I thought there would be no non-bonded contribution. I use a very high cut-off (longer than chain length) and no pbc. Am i missing something ?<br>
<br>
</blockquote>
<br></div>
Without seeing your .mdp file and the actual energy terms you're observing, I can only guess. One would think that if it is the only molecule in the system, there should be no intermolecular Coulombic terms (unless maybe some arise due to periodicity, but in that case you do not have an infinite system and then they are artifacts). There may be intramolecular terms (like 1-4) or PME-related terms.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey <<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a> <mailto:<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>>> wrote:<br>
<br>
I was not sure if changing the size of maxcg would not negatively<br>
influence anything else. I will give it a try. Thanks Justin<br>
<br>
<br>
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Amit Choubey wrote:<br>
<br>
I change the maximum charge group size defined in the<br>
include/types/nblist.h header from 32 to 267. Then grompp<br>
worked fine but the mdrun did not start. The following error<br>
came out<br>
<br>
Program mdrun_jptlc, VERSION 4.5.3<br>
Source code file: ns.c, line: 2417<br>
<br>
Fatal error:<br>
Max #atoms in a charge group: 267 > 64<br>
<br>
<br>
/* Verify whether largest charge group is <= max cg.*<br>
* This is determined by the type of the local exclusion<br>
type *<br>
* Exclusions are stored in bits. (If the type is not large*<br>
* enough, enlarge it, unsigned char -> unsigned short<br>
-> unsigned long)*<br>
*/<br>
<br>
<br>
The solution is described in the comment above.<br>
<br>
<br>
maxcg = sizeof(t_excl)*8;<br>
<br>
<br>
Increase the size here.<br>
<br>
-Justin<br>
<br>
<br>
if (nr_in_cg > maxcg)<br>
{<br>
gmx_fatal(FARGS,"Max #atoms in a charge group: %d ><br>
%d\n",<br>
nr_in_cg,maxcg);<br>
}<br>
<br>
<br>
-- ==============================<u></u>__==========<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></div></div>
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==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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