Dear all :)<br><br>I have one extra question about Genion.<br><br>I want to neitralise my system with the qtot - 1.550002e by placing some Na and Cl ions under the physiological concetrantion 100 mmol/l<br><br>I've performed<br>
<br>genion -s ions.tpr -o b2ar_ions.gro -p topol.top -pname NA -nname CL -conc 0.1 -neutral<br><br>but insytead I've obtained system with 4.499977e-01 changre<br><br>What should I do to fix this problem?<br><br>James<br>
<br><div class="gmail_quote">2012/2/16 Kathleen Kirchner <span dir="ltr"><<a href="mailto:kirchner@mis.mpg.de" target="_blank">kirchner@mis.mpg.de</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear James,<br>
<br>
I was working for a longer time on ion placement within more or less equilibrated structures. I found my nearly magical miracle solving those problems in not using any gromacs tool for producing the input structure but rather use the free software Packmol:<br>
<br>
<a href="http://www.ime.unicamp.br/%7Emartinez/packmol/" target="_blank">http://www.ime.unicamp.br/~<u></u>martinez/packmol/</a><br>
<br>
The software solves a mathematical minimization problem instead of putting somewhere molecules and deleting others.<br>
<br>
After a short energy minimization of the obtained output structure (a few 100 steps of steep algorithm) usally my systems work fine.<br>
<br>
Best<span><font color="#888888"><br>
Kathleen<br>
<br>
<br>
-- <br>
Kathleen Kirchner<br>
PhD student<br>
Max Planck Institute for Mathematics in the Sciences<br>
(MPI f. Mathematik in den Naturwissenschaften)<br>
Inselstr. 22-26, D04103 Leipzig<br>
e-mail: <a href="mailto:kirchner@mis.mpg.de" target="_blank">kirchner@mis.mpg.de</a><br>
web: <a href="http://www.mis.mpg.de/scicomp/CompPhysChem/" target="_blank">http://www.mis.mpg.de/scicomp/<u></u>CompPhysChem/</a><br>
Tel +49 341 9959 725<br>
Fax +49 341 9959 999</font></span><div><div><br>
<br>
-- <br>
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