Hi sir,<br>
Thanks alot for your valuable suggestion .<br>
<br>
As i was actually searching a way to find out the missing bond but i
could not find .can u please suggest me a way where i can further
proceed to find it.<br>
<br>
Thanks in advance.<br>
<br>
<br>
Regards<br>
Rajitha.<br><br><br><br><br><br><br><div class="gmail_quote">On Thu, Dec 22, 2011 at 4:30 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Today's Topics:<br>
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1. Re: Re:comparison of energy between GROMACS and NAMD<br>
(David van der Spoel)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 22 Dec 2011 09:32:04 +0100<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] Re:comparison of energy between GROMACS and<br>
NAMD<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:E5174BF1-6349-44AE-AD8B-2898CEB50898@xray.bmc.uu.se">E5174BF1-6349-44AE-AD8B-2898CEB50898@xray.bmc.uu.se</a>><br>
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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>
> On 12/22/2011 6:16 PM, Sairam Tatikonda wrote:<br>
>><br>
>> 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>
><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>
>><br>
>> NAMD (kcal/mol) GROMACS(kcal/mol)<br>
>> Bond 1929.3647 1928.57<br>
>> pro.dihed 256.1007 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>
><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>
<br>
It would be useful to see where the missing bond is, considering that the number of atoms is the same.<br>
In principle there could be a bug in the charmm rtp files for instance.<br>
<br>
>><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 href="http://terms.is" target="_blank">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>
><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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