<div>Hi Justin,</div>
<div>Thanks for comments,<br></div>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 8:21 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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi all,<br>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:<br>
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45<br>System total charge: 0.000<br>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!<br>
Now my questions are:<br>(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.<br></blockquote><br></div>Can you post your exact command line? </blockquote>
<div>my command is:</div>
<div>genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol 1 -ci insert.gro</div>
<div>I also tried <br>
<div>genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol 1 -ci insert.gro -try 100</div>
<div>by using 20,30,40...,100 but each time was the same. (I also did it without shell command but no success)</div></div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span>
<div class="im"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">(2) This command will try to add water where? In the same coordinates as insert.gro??<br></blockquote><br>
</div>From genbox -h:<br><br>"3) Insert a number (-nmol) of extra molecules (-ci) at random positions. The<br>program iterates until nmol molecules have been inserted in the box. To test<br>whether an insertion is successful the same VanderWaals criterium is used as<br>
for removal of solvent molecules. When no appropriately sized holes (holes<br>that can hold an extra molecule) are available the program tries for -nmol *<br>-try times before giving up. Increase -try if you have several small holes to<br>
fill."</blockquote>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><font color="#888888"><span id=""></span><br>-Justin<br><br></font>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">What is your suggestions?? Many Thanks in Advance/Jamie<br><br></div>
<div class="im">On Thu, Aug 13, 2009 at 5:25 PM, Vitaly V. Chaban <<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a> <mailto:<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>>> wrote:<br>
<br> 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><br><br> Vitaly<br><br><br> ><br> >> Thanks for the answer. When I said far away means my pore was in<br> 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><br><br><br></div>------------------------------------------------------------------------
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<div class="im">-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>
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