thanks a bunch for the input.<br><br><div class="gmail_quote">On Thu, Sep 10, 2009 at 9:38 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
hi everyone,<br>
<br>
I guess if i knew the exact format of .gro files i could write a small code to copy data from pdb to gro . I cannot find this info anywhere. I believe that it has co-ordinates and velocities but how are the velocities choose (randomly?). I am also not sure abt the exact order.<br>
<br>
</blockquote>
<br></div>
The format is available as part of the online manual:<br>
<br>
<a href="http://manual.gromacs.org/current/online/gro.html" target="_blank">http://manual.gromacs.org/current/online/gro.html</a><br>
<br>
Although I don't know why you feel it necessary to write code that's already part of editconf.<br>
<br>
Velocities are assigned randomly when grompp sees "gen_vel = yes" in the .mdp file, according to the gen_temp parameter. I'd say keep life easy and use the functions Gromacs already provides you instead of writing code for converting coordinates and writing velocities :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Amit<div class="im"><br>
<br>
On Wed, Sep 9, 2009 at 5:29 PM, Amit Choubey <<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a> <mailto:<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>>> wrote:<br>
<br>
hi everyone,<br>
<br>
I have a pdb file of my system and i want it to be fed into the<br>
GROMACS software. I have a new force field for the simulation and i<br>
have made the .top file manually which includes the new library FF<br>
files. I need to get a .gro file from the .pdb file that i have. So,<br>
is there a way out to do this without incorporating pdb2gmx because<br>
i dont use the standard FF and i dont really have all the other<br>
datafiles for the new FF except for necessary bond and nonbonded infos.<br>
<br>
Amit<br>
<br>
<br>
<br></div>
------------------------------------------------------------------------<div class="im"><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>
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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