On 2011-12-22 13:24, Sairam Tatikonda wrote:
Hi sir,
Thanks alot for your valuable suggestion .
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.
Thanks in advance.
The top file lists all the bonds in order.
I guess the same information must be in the psf file?
Regards
Rajitha.
On Thu, Dec 22, 2011 at 4:30 PM, <[email protected]
<mailto:[email protected]>> wrote:
Send gmx-users mailing list submissions to
[email protected] <mailto:[email protected]>
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
[email protected] <mailto:[email protected]>
You can reach the person managing the list at
[email protected] <mailto:[email protected]>
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
Today's Topics:
1. Re: Re:comparison of energy between GROMACS and NAMD
(David van der Spoel)
----------------------------------------------------------------------
Message: 1
Date: Thu, 22 Dec 2011 09:32:04 +0100
From: David van der Spoel <[email protected]
<mailto:[email protected]>>
Subject: Re: [gmx-users] Re:comparison of energy between GROMACS and
NAMD
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset="us-ascii"
On Dec 22, 2011, at 9:05 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
> On 12/22/2011 6:16 PM, Sairam Tatikonda wrote:
>>
>> Hi,
>> 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
>
> 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.
>
>>
>> NAMD (kcal/mol)
GROMACS(kcal/mol)
>> Bond 1929.3647 1928.57
>> pro.dihed 256.1007 345.21
>> imp dihed 10.8044 10.797
>> potential 1295 1215
>> coloumbic -1483.6554 -1557.72
>> LJ 73.1648 69.445
>>
>> Structure
>> information NAMD GROMACS
>> atoms 1231 1231
>> bonds 1237 1236
>> dihedrals 3293 3292
>> Impr dihedrals 204 203
>
> It seems clear that you have a difference in the .psf and .top
topologies you are generating, so any further comparison is not
profitable.
>
It would be useful to see where the missing bond is, considering
that the number of atoms is the same.
In principle there could be a bug in the charmm rtp files for instance.
>>
>> 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.
>> where i have calculated the coloumbic energy and LJ energy from
log file of GROMACS by adding up short range,long range and 14
terms.is <http://terms.is> it the correct way of calculating the
total coloumbic and LJ energies to compare them with NAMD coloumbic
and LJ values.
>
> 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.
>
> Mark
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
> --
> gmx-users mailing list [email protected]
<mailto:[email protected]>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [email protected]
<mailto:[email protected]>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20111222/818a5c0c/attachment-0001.html
------------------------------
--
gmx-users mailing list
[email protected] <mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
End of gmx-users Digest, Vol 92, Issue 116
******************************************
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
