<div>Dear Gmx users,</div>
<div>Does any one know why genbox stops when I use this command:</div>
<div>"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"</div>
<div>or when I use this command:</div>
<div>"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"</div>
<div>It goes until </div>
<div>Reading solvent configuration </div>
<div>Solvent configuration contains 648 atoms in 216 residues</div>
<div>and then stops....</div>
<div>Would you please let me know why it happens?? Many Thanks in Advance/Jamie</div>
<div><br><br> </div>
<div class="gmail_quote">On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed <span dir="ltr"><<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@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">
<div>Thanks to Justin & Mark for answering my second question...</div>
<div>Could any one give me a hint on my first question that I copy it again?</div>
<div>--about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration.
<div class="im"><br>Integral 1 0.01595<br>set average<br>SS1 3.718082e-04<br></div>
<div class="im">Would you please inform me what are these number and what is the relation between them?<br></div>
<div class="im">Many Thanks in Advance/Jamie<br><br></div></div>
<div>
<div></div>
<div class="h5">
<div class="gmail_quote">On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><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">Dear Gmx Users,<br>I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration.<br>
Integral 1 0.01595<br>set average<br>SS1 3.718082e-04<br>--1) Would you please inform me what are these number and what is the relation between them?<br> <br></blockquote><br></div>Can't comment on the first part...maybe the code will point you in the right direction?
<div><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">--2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot <br>
</blockquote><br></div>This task might be approached in a couple of ways:<br><br>1. genconf -nbox to define a suitable number of replicate systems.<br>2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie<br><br><br></div>------------------------------------------------------------------------
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<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>
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