Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is working normally...??!! Do you have any idea?<br><br>
<div class="gmail_quote">On Sun, Oct 11, 2009 at 1:52 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">I converted spc216.pdb to gro using editconf. SO they must be the <br></blockquote><br></div>I suppose that's fine, I just don't see all the need for interconverting file formats. It just opens up the possibility of more errors if you don't keep track of what you're doing :)
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">same(?). The version is 4.0.5 ...it was fine before... yes ran it just now for fws tuto... how long it takes time in your machine?<br>
</blockquote><br></div>I have the same version. The commands you showed completed in just a fraction of a second, like most simple solvation procedures.<br><font color="#888888"><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"><br>On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Jamie Seyed wrote:<br><br> Hi Justin,<br> yes resize.gro is a created file from editconf which has box<br> size of 5.05918 on the last line<br> my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"<br>
<br><br> Do you actually have separate spc216.pdb and spc216.gro files? Just<br> trying to make sure this actually worked.<br><br><br> and for second command I changed 1 to 5 but it still stops in<br> the same point. I am trying to examine 2 methods that you & Mark<br>
suggested me to<br><br><br> Very weird. Both of your commands worked on my machine. What<br> version of Gromacs are you using? Does genbox work for other systems?<br><br> -Justin<br><br> create a box of water.../Many Thanks/Jamie<br>
<br> On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
</div>
<div class="im"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br><br><br><br> Jamie Seyed wrote:<br>
<br></div>
<div>
<div></div>
<div class="h5"> 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<br> topol.top"<br>
or when I use this command:<br> "genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p<br> 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<br> Advance/Jamie<br><br>
<br> Is "resize.gro" a new file? Or something you have created before<br> (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<br>
certainly too small to contain 500 solvent molecules. Define an<br> appropriate box size.<br><br> -Justin<br><br><br> On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed<br> <<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>><br>
<mailto:<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>>><br> <mailto:<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a><br>
<mailto:<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><br> <mailto:<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>>>>><br>
<br> wrote:<br><br> Thanks to Justin & Mark for answering my second<br> question...<br> Could any one give me a hint on my first question that<br> I copy<br> it again?<br>
--about g_velacc and calculating the diffusion<br> constant from<br> that.<br> In mailing list people say that we need to divide it<br> by mass<br> squared<br>
and 1/3. Then I found another recent post that said it<br> has been<br> included in the code... Would you please clarify this<br> that if<br> I need<br> the factors or not. Also I found 2 numbers after<br>
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<br> 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<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <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<br> calculating<br> the diffusion constant from that. In mailing list<br>
people say<br> that we need to divide it by mass squared and<br> 1/3. Then I<br> found another recent post that said it has been<br> included in<br>
the code... Would you please clarify this that<br> if I<br> need the<br> factors or not. Also I found 2 numbers after<br> integration.<br> Integral 1 0.01595<br>
set average<br> SS1 3.718082e-04<br> --1) Would you please inform me what are these<br> number and<br> what is the relation between them?<br>
Can't comment on the first part...maybe the code will<br> point you<br> in the right direction?<br><br><br> --2) My second question is I want to make a<br>
box of only<br> water (spce) with let say 500 water molecules.<br> Would you<br> please give me quick hints how to do it (the<br> proper<br> way) or<br>
refer me to good point? Up to now I can only<br> have 216<br> 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<br> replicate<br> systems.<br> 2. genbox -box -maxsol 500 to define a<br> 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<br> make it... I<br> appreciate if you help me to understand the first<br> issue and<br>
be able to overcome the second one. Many Thanks in<br> Advance/Jamie<br><br><br> ------------------------------------------------------------------------<br>
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<br><br> -- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> Department of Biochemistry<br> Virginia Tech<br>
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<div class="h5"> -- ========================================<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> <<a href="http://vt.edu/" target="_blank">http://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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<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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