<html><head></head><body bgcolor="#FFFFFF"><div><br></div><div><br>On Dec 22, 2011, at 9:05 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>
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On 12/22/2011 6:16 PM, Sairam Tatikonda wrote:
<blockquote cite="mid:CAPc5CMN2SMWtY6khn7VDCUFg5bDaf95jdhFf4t1-Nm7mQ9bBZQ@mail.gmail.com" type="cite">Hi,<br>
I have performed minimization of ubiquitin in vaccum both in
GROMACS and NAMD using CHARMM force field .when i have compared
the energy values for first step ,i found that variation in the
values<br>
</blockquote>
<br>
In GROMACS, that energy is based on the result of the first EM step.
To do a "single-point" energy calculation, do a zero-step MD run, or
use mdrun -rerun.<br>
<br>
<blockquote cite="mid:CAPc5CMN2SMWtY6khn7VDCUFg5bDaf95jdhFf4t1-Nm7mQ9bBZQ@mail.gmail.com" type="cite"><br>
NAMD (kcal/mol)
GROMACS(kcal/mol)<br>
Bond 1929.3647 1928.57<br>
pro.dihed <span class="Object" id="OBJ_PREFIX_DWT36">256.1007</span>
345.21<br>
imp dihed 10.8044 10.797<br>
potential 1295 1215<br>
coloumbic -1483.6554 -1557.72<br>
LJ 73.1648
69.445 <br>
<br>
Structure<br>
information NAMD GROMACS<br>
atoms 1231 1231<br>
bonds 1237 1236<br>
dihedrals 3293 3292<br>
Impr dihedrals 204 203<br>
</blockquote>
<br>
It seems clear that you have a difference in the .psf and .top
topologies you are generating, so any further comparison is not
profitable.<br>
<br></div></blockquote><div><br></div>It would be useful to see where the missing bond is, considering that the number of atoms is the same.<div>In principle there could be a bug in the charmm rtp files for instance.</div><div><br><blockquote type="cite"><div>
<blockquote cite="mid:CAPc5CMN2SMWtY6khn7VDCUFg5bDaf95jdhFf4t1-Nm7mQ9bBZQ@mail.gmail.com" type="cite"><br>
Though the number of atoms are same ,i did not understand why
there is variation in number of bonds,angles and dihedrals leading
to difference in energy values. <br>
where i have calculated the coloumbic energy and LJ energy from
log file of GROMACS by adding up short range,long range and 14 <a moz-do-not-send="true" href="http://terms.is">terms.is</a> it
the correct way of calculating the total coloumbic and LJ energies
to compare them with NAMD coloumbic and LJ values.<br>
</blockquote>
<br>
You will have to read the documentation for each code carefully in
order to do calculations that compute the same things. There are
lots of details you will have to get exactly right.<br>
<br>
Mark<br>
<br>--
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