<div>Hi all,</div>
<div>Thanks for your comments. Actually as Vitaly mentioned I am still try to visualize the gro-file made by genbox. I found out for any number that I use for "-nmol ? -ci insert.gro" after some iterations and upto these values:</div>
<div>Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45<br>System total charge: 0.000</div>
<div>I get segmentation fault. In fact cut-off values from 0.1 in the case of -nmol 0, jumps to 0.45 in the case of -nmol 1 and then it gives me segmentation fault. The only way to get rid of it is put -nmol 0!</div>
<div>Now my questions are:</div>
<div>(1) What can be wrong in my insert.gro file. Does it matter the coordinates of 1 molecule that I obtained from spc216.gro file?? The format is the same.</div>
<div>(2) This command will try to add water where? In the same coordinates as insert.gro??</div>
<div>What is your suggestions?? Many Thanks in Advance/Jamie<br><br></div>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 5:25 PM, Vitaly V. Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Tsjerk,<br><br>I understood the situation in such a way that MD was not run at all,<br>so Jamie visualizes *gro* file obtained with *genbox*...<br>
<br>Jamie,<br>didn't you look at this: <a href="http://www.ime.unicamp.br/~martinez/packmol/" target="_blank">http://www.ime.unicamp.br/~martinez/packmol/</a><br>to prepare your system?<br><font color="#888888"><br><br>
Vitaly<br></font>
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<div class="h5"><br><br>><br>>> Thanks for the answer. When I said far away means my pore was in one corner<br>>> of vmd window and the water molecules in opposite corner (almost).<br>><br>> Did I miss something or did neither Vitaly nor Justin reply "Are you<br>
> perhaps seeing the effect of periodic boundary conditions?".<br>><br>> Tsjerk<br>><br>> --<br>> Tsjerk A. Wassenaar, Ph.D.<br>> Junior UD (post-doc)<br>> Biomolecular NMR, Bijvoet Center<br>
> Utrecht University<br>> Padualaan 8<br>> 3584 CH Utrecht<br>> The Netherlands<br>> P: +31-30-2539931<br>> F: +31-30-2537623<br></div></div></blockquote></div><br>