Hi <br><br>this a part of the md.log where the system has -50 charge<br><br> two-body bonded interactions: 0.407 nm, Bond, atoms 514 515<br> multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275<br>Minimum cell size due to bonded interactions: 0.804 nm<br>
Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm<br>Estimated maximum distance required for P-LINCS: 0.810 nm<br>This distance will limit the DD cell size, you can override this with -rcon<br>Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm<br>
The maximum allowed number of cells is: X 11 Y 11 Z 11<br>Domain decomposition grid 4 x 1 x 1, separate PME nodes 0<br>Domain decomposition nodeid 0, coordinates 0 0 0<br><br>Table routines are used for coulomb: TRUE<br>Table routines are used for vdw: TRUE<br>
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm<br>Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2<br><span style="background-color: rgb(255, 153, 0);">System total charge: -50.000</span><br>Generated table with 1100 data points for Shift.<br>
Tabscale = 500 points/nm<br>Generated table with 1100 data points for LJ6Shift.<br>Tabscale = 500 points/nm<br>Generated table with 1100 data points for LJ12Shift.<br>Tabscale = 500 points/nm<br>Configuring nonbonded kernels...<br>
Configuring standard C nonbonded kernels...<br>Testing ia32 SSE2 support... present<br><br><div class="gmail_quote">On Tue, Jul 26, 2011 at 2:18 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Sara baretller 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 used the genion command using like this "genion -s file.tpr -conc 0.2 -neutral -o file.gro -random " again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command.<br>
<br>
so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . <br>
</blockquote>
<br></div>
Please copy and paste the exact (pertinent) output from the log file.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Sara<div><div></div><div class="h5"><br>
<br>
<br>
<br>
On Tue, Jul 26, 2011 at 1:05 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>
Sara baretller wrote:<br>
<br>
Hi all<br>
<br>
I used the genion to add a concentration and to neutalize the<br>
system in the same time by using the<br>
<br>
*genion -s file.tpr -conc 0.2 -neutral -o file.gro -random<br>
so it did add the NA and Cl but it did not neutralize the<br>
system, the net charge of the system still the same negative.<br>
<br>
<br>
I find this hard to believe. The application of genion -conc<br>
-neutral has worked in every instance I've tried it along every<br>
Gromacs version. Check your output again.<br>
<br>
<br>
so i tried to use the genion seperate to neutralize the<br>
charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions<br>
added for the concentration.<br>
<br>
<br>
Without the actual sequence of commands, this is not a useful<br>
description. genion adds ions based on whatever it finds in the .tpr<br>
file (which is presumably not neutralized). If you do not re-create<br>
a .tpr file in between different additions of ions, you're going to<br>
be undoing work you thought you did.<br>
<br>
-Justin<br>
<br>
-- ==============================<u></u>__==========<br>
<br>
Justin A. Lemkul<br>
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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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