Re: [gmx-users] Distance restraint energy terms
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 ? 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 listgmx-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 Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!. The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-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
Re: [gmx-users] Distance restraint energy terms
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 listgmx-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
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 listgmx-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
[gmx-users] Distance restraint energy terms
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. I have following 2 questions: 1. How one should ensure that the restraints are applied correctly ? 2. How should I check the corresponding energy ? Plz help ASAP Regards, Nikhil Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- gmx-users mailing listgmx-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
