hello Tsjerk,<br>thanks for the reply... the syntax of g_density is such that we need to provide a tpr file right... is there a way of doing it without the tpr... and also from where are the radii of the atoms read for calculation of the volume... or is the volume calculated differently...<br>
thanks in advance<br><br>Regards,<br>Jagan<br><br><div class="gmail_quote">On Sat, Jun 6, 2009 at 3:10 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">Hi Jagan,<br>
<br>
If you provide a .tpr file, the masses will be read from there.<br>
Otherwise, when providing a .gro/.pdb file or so, masses will be read<br>
from the file atommass.dat in the GMX library directory.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Sat, Jun 6, 2009 at 11:25 AM, Jagan Mohan<<a href="mailto:o.jagan@gmail.com">o.jagan@gmail.com</a>> wrote:<br>
> Hey everyone,<br>
> I would like to know from where does the g_density read the masses and radii<br>
> of atoms to calculate the density... We do provide a tpr file but from where<br>
> does it refer to and add these masses... I have a system for which i have a<br>
> topology... i use this for the generation of tpr but will the masses be<br>
> considered from this topology... Please do help me out...<br>
><br>
> Thanks in advance<br>
><br>
> Regards,<br>
> Jagan<br>
><br>
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<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
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</blockquote></div><br><br clear="all"><br>-- <br>-{[O]}-<br>