<div>Hi Justin,</div>
<div>yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line</div>
<div>my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"</div>
<div>and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you & Mark suggested me to create a box of water.../Many Thanks/Jamie<br><br></div>
<div class="gmail_quote">On Sun, Oct 11, 2009 at 12:54 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">Dear Gmx users,<br>Does any one know why genbox stops when I use this command:<br>"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"<br>
or when I use this command:<br>"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"<br>It goes until<br>Reading solvent configuration<br>Solvent configuration contains 648 atoms in 216 residues<br>
and then stops....<br>Would you please let me know why it happens?? Many Thanks in Advance/Jamie<br><br></blockquote><br></div>Is "resize.gro" a new file? Or something you have created before (i.e., an empty file with a box size defined)?<br>
<br>Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size.<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 class="im"><br> On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed <<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a> <mailto:<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>>> wrote:<br>
<br> Thanks to Justin & Mark for answering my second question...<br> Could any one give me a hint on my first question that I copy it again?<br> --about g_velacc and calculating the diffusion constant from that.<br>
In mailing list people say that we need to divide it by mass squared<br> and 1/3. Then I found another recent post that said it has been<br> included in the code... Would you please clarify this that if I need<br> the factors or not. Also I found 2 numbers after integration.<br>
<br> Integral 1 0.01595<br> set average<br> SS1 3.718082e-04<br> Would you please inform me what are these number and what is the<br> relation between them?<br> Many Thanks in Advance/Jamie<br><br> On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
</div>
<div>
<div></div>
<div class="h5"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br><br><br><br> Jamie Seyed wrote:<br><br> Dear Gmx Users,<br> I have a 2 questions. First about g_velacc and calculating<br>
the diffusion constant from that. In mailing list people say<br> that we need to divide it by mass squared and 1/3. Then I<br> found another recent post that said it has been included in<br>
the code... Would you please clarify this that if I need the<br> 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<br> what is the relation between them?<br> <br><br> Can't comment on the first part...maybe the code will point you<br> in the right direction?<br>
<br><br> --2) My second question is I want to make a box of only<br> water (spce) with let say 500 water molecules. Would you<br> please give me quick hints how to do it (the proper way) or<br>
refer me to good point? Up to now I can only have 216 water<br> molecules from tuto/water folder and I tried a lot<br><br><br> 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<br> fill it with only the desired number of molecules.<br><br> -Justin<br><br> to start from the beginning, but I could not make it... I<br>
appreciate if you help me to understand the first issue and<br> be able to overcome the second one. Many Thanks in Advance/Jamie<br><br><br> ------------------------------------------------------------------------<br>
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<div class="h5"><br>-- <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>
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