sorry i did not mention it but the E field contribution should be zero, i am sure about it. Also when i make all the cutoff = 0 the energy terms are<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 1.03128e+06 1.03128e+06</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> 7.49142e-02 0.00000e+00 0.00000e+00 1.03104e+06 1.03104e+06</div><div> Pressure (bar)</div><div> 0.00000e+00</div><div>
<br></div><div>Coulomb (SR) is quite close but not exactly equal to previous case when cutoff is 60 nm.</div><br><div class="gmail_quote">On Sun, Aug 14, 2011 at 1:57 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><div></div><div class="h5"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Following is the mdp file<br>
<br>
cpp = /usr/bin/cpp<br>
;define = -DFLEX_SPC<br>
constraints = none<br>
integrator = steep<br>
nsteps = 10000<br>
;<br>
; Energy minimizing stuff<br>
;<br>
emtol = 200<br>
emstep = 0.01<br>
pbc = no<br>
nstcomm = 0<br>
ns_type = grid<br>
coulombtype = Cut-off rlist = 60<br>
rcoulomb = 60<br>
rvdw = 60<br>
Tcoupl = no<br>
Pcoupl = no<br>
gen_vel = no<br>
<br>
E_x = 1 0 0<br>
E_y = 1 0 0<br>
E_z = 1 0 0<br>
<br>
<br>
Following is the energy term<br>
<br>
Step Time Lambda<br>
0 0.00000 0.00000<br>
<br>
Energies (kJ/mol)<br>
Bond Angle LJ (SR) Coulomb (SR) Potential<br>
1.11496e-07 0.00000e+00 0.00000e+00 9.90561e+05 9.90561e+05<br>
Pressure (bar)<br>
0.00000e+00<br>
<br>
Step Time Lambda<br>
1 1.00000 0.00000<br>
<br>
Energies (kJ/mol)<br>
Bond Angle LJ (SR) Coulomb (SR) Potential<br>
7.55922e-02 0.00000e+00 0.00000e+00 9.90324e+05 9.90324e+05<br>
Pressure (bar)<br>
0.00000e+00<br>
<br>
<br>
</blockquote>
<br></div></div>
I suspect that energy terms comes from the use of an electric field, which you had not mentioned before.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Amit<div class="im"><br>
<br>
On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Amit Choubey wrote:<br>
<br></div><div class="im">
Justin, when i define the whole line charge as a charge group i<br>
do get a coulomb energy contribution. I thought there would be<br>
no non-bonded contribution. I use a very high cut-off (longer<br>
than chain length) and no pbc. Am i missing something ?<br>
<br>
<br>
Without seeing your .mdp file and the actual energy terms you're<br>
observing, I can only guess. One would think that if it is the only<br>
molecule in the system, there should be no intermolecular Coulombic<br>
terms (unless maybe some arise due to periodicity, but in that case<br>
you do not have an infinite system and then they are artifacts).<br>
There may be intramolecular terms (like 1-4) or PME-related terms.<br>
<br>
-Justin<br>
<br>
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey<br>
<<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>><br></div><div class="im">
<mailto:<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<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<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> <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<br>
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<br>
exclusion<br>
type *<br>
* Exclusions are stored in bits. (If the type is<br>
not large*<br>
* enough, enlarge it, unsigned char -> unsigned<br>
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<br>
group: %d ><br>
%d\n",<br>
nr_in_cg,maxcg);<br>
}<br>
<br>
<br>
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