<br><br><div class="gmail_quote">On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br><br>----- Original Message -----<br>From: oguz gurbulak <<a href="mailto:gurbulakoguz@yahoo.com" target="_blank">gurbulakoguz@yahoo.com</a>><br>Date: Thursday, September 30, 2010 21:38<br>Subject: [gmx-users] NAMD simulation in Gromacs<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><br></div><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font:inherit" valign="top"><div class="im"> <p class="MsoNormal">
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>Dear All,</p> <p class="MsoNormal"> </p> <p class="MsoNormal" style="text-align:justify">> I performed a 50 ns md simulation using NAMD and want to continue this simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation in Gromacs ? If so, could you please give me the information about this process ? <br>
</p><p class="MsoNormal" style="text-align:justify"><br></p></div><p class="MsoNormal" style="text-align:justify">Not really. You would need to generate a .top in the normal way, and this process cannot use any topology information that NAMD was using. You could start the GROMACS simulation from the endpoint of the NAMD simulation, but it would not be continuous in any sense.<br>
</p></td></tr></tbody></table></blockquote><div><br></div><div>We have a patch to psfgen to generate gromacs topology. We plan to put this on our website. While it hasn't be uploaded yet, please write me in case you would like to have a copy. It does convert the parameter files. We use Pär's scripts to do that part.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font:inherit" valign="top"><div class="im">
<p class="MsoNormal" style="text-align:justify"></p> <p class="MsoNormal" style="text-align:justify">Secondly can I convert NAMD output files into gromacs output files and use gromacs analysis tools ? Could you please also give me the information about this issue ?</p>
<p class="MsoNormal"> </p></div><p class="MsoNormal">If you have VMD installed then GROMACS is supposed to be able to link to its libraries to enable GROMACS tools to read any file format that VMD can read, which will include all NAMD formats. I'm unaware that anybody has written any documentation about this, however. That's probably the path of least resistance.</p>
</td></tr></tbody></table></blockquote><div><br></div><div>Yes as long as VMD is installed (and GROMACS is compiled with DLOPEN support - which is default) all the GROMACS tools automatically can read most VMD supported format. The exception is any format which doesn't record the number of atoms (as e.g. Amber).</div>
<div><br></div><div>Roland</div><div> </div></div>