On 08/02/10 16:18, nikhil damle wrote:
I think I could figure out the mistake I was committing.
I intended to restrain 2 pairs of distances simultaneously. Hence the
index of both the pairs were kept 1 with lower and upper bounds
different for the two pairs. This had created error. The same indices
for a pair of distances would imply they contribute to same NOE signal.
Hence their lower and upper bounds should be same. I thought the same
index would only mean that the restraints on both pairs would be treated
simultaneously as written in manual and there is no need that lower and
upper bounds of the restraints should be equal for both pairs.
Am I understanding correctly ?
You'll stand a better chance of a useful answer if you quote your usage
of such indices in your .itp file. Manual 4.3.4 has an example.
Mark
Regards,
Nikhil
------------------------------------------------------------------------
*From:* nikhil damle <pdnik...@yahoo.co.in>
*To:* jalem...@vt.edu; Discussion list for GROMACS users
<gmx-users@gromacs.org>
*Sent:* Mon, 8 February, 2010 10:14:10 AM
*Subject:* Re: [gmx-users] Distance restraint energy terms
I have already included the [distance_restraints] section in .top file.
In principle fac coloumn should be multiplied with the default force
constant (1000 Kj Mol-1 nm-2) and that should get reflected in the
mdout.mdp file. But this does not happen. mdout.mdp file still depicts
the force constant to be 1000 even though fac coloumn > 1. I wish to
restrain the distance between on two atoms.
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Sat, 6 February, 2010 6:10:12 PM
*Subject:* Re: [gmx-users] Distance restraint energy terms
nikhil damle wrote:
> Hi,
>
> I have applied distance restraints on my system during MD simulation
through following options:
> "disre = simple" and disre_fc = 2000 in .mdp file.
> Now i wish to see the energy term corresponding to these restraints
in principle to be written in .edr file. But g_energy programme does not
list any term corresponding to these restraints.
>
Then you haven't applied any distance restraints.
> I have following 2 questions:
> 1. How one should ensure that the restraints are applied correctly ?
> 2. How should I check the corresponding energy ?
>
Setting distance restraints isn't as simple as setting some .mdp
options, you have to have a [distance_restraints] section in the
topology that describes exactly what those restraints are. This is all
in the manual, and has been discussed a number of times on the list, so
there should also be some pointers in the archives.
If it works, you should see the corresponding energy term.
-Justin
> Plz help ASAP
>
> Regards,
> Nikhil
>
>
> ------------------------------------------------------------------------
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage
<http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/>.
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!
<http://in.rd.yahoo.com/tagline_ie8_new/*http://downloads.yahoo.com/in/internetexplorer/>.
------------------------------------------------------------------------
The INTERNET now has a personality. YOURS! See your Yahoo! Homepage
<http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/>.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
