<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>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.<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, 6 February, 2010 6:10:12 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Distance restraint energy terms<br></font><br><br><br>nikhil damle wrote:<br>> Hi,<br>> <br>> I have applied distance restraints on my system during MD simulation through following options:<br>> "disre = simple" and disre_fc = 2000 in .mdp file.<br>> 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.<br>> <br><br>Then you haven't applied any distance restraints.<br><br>> I have following 2 questions:<br>> 1. How one should ensure that the restraints are applied correctly ?<br>> 2. How should I check the corresponding energy ?<br>> <br><br>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.<br><br>If it works, you should see the corresponding energy term.<br><br>-Justin<br><br>> Plz help ASAP<br>> <br>> Regards,<br>> Nikhil<br>> <br>> <br>> ------------------------------------------------------------------------<br>> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage <<a href="http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/" target="_blank">http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/</a>>.<br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg,
VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php"
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