<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Thanks, Justin. I'll do experiments on that. </DIV>
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<DIV> <B>Thu, 7/7/11, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] placing dihedral constraints<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Thursday, July 7, 2011, 1:32 AM<BR><BR>
<DIV class=plainMail><BR><BR>Mr Bernard Ramos wrote:<BR>> <BR>> Hi Mark and everyone!<BR>> This has been a previous topic though and thanks Mark for the reply.<BR>> What I need to do is to calculate the potential energy (energy minimzation) of a molecule at every fixed pairs of dihedrals (phi, psi). I did the suggestions on _<A href="http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints_" target=_blank>http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints_</A>. In fact what follows is the entry I placed in my topol.top<BR>> [ dihedral_restraints ]<BR>> ; ai aj ak al type label phi dphi kfac power<BR>> 5 1 40 38 1 1 30 0 1 2<BR>> 12 40 38 34 1 1 10 0 1
2<BR>> I also added the following in my mdp file<BR>> dihre = yes<BR>> dihre_fc = 10000<BR>> I removed disre_tau and nstdihreout as they are no longer needed in the recent gromacs versions. Unfortunately, after checking the dihedral angles, they appear to be far from the set value of (phi=30, psi=10). I understand that we are restraining the angles and not constraining/fixing them. Is there a way we can have the resulting phi and psi as close to the required values? I get values 15 degrees away <BR><BR>Increase kfac or dihre_fc. Probably the initial geometry doesn't like the restraint being placed there so you may have to increase the energy penalty for deviating from the restrained value.<BR><BR>> from the original settings. Your help is greatly appreciated.<BR>> One more question. This restraining will not affect the final potential energy right?<BR><BR>Certainly it will. You'd be preventing (or at the very
least, disfavoring) EM from adjusting surrounding coordinates. Such a procedure may have a positive or negative outcome on the final energy.<BR><BR>-Justin<BR><BR>> Bernard<BR>> <BR>> --- On *Mon, 6/27/11, Mark Abraham /<<A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=Mark.Abraham@anu.edu.au" ymailto="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</A>>/* wrote:<BR>> <BR>> <BR>> From: Mark Abraham <<A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=Mark.Abraham@anu.edu.au" ymailto="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</A>><BR>> Subject: Re: [gmx-users] placing dihedral constraints<BR>> To: "Discussion list for GROMACS users" <<A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>>
Date: Monday, June 27, 2011, 5:38 PM<BR>> <BR>> On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote:<BR>>> Hi!<BR>>> <BR>>> I would like to freeze two dihedrals/torsion angles but allow the<BR>>> rest (i.e. bonds, angles) to relax during energy minimization and<BR>>> MD. How do I go over applying constraints? Thanks.<BR>>> <BR>> <BR>> See<BR>> <A href="http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints" target=_blank>http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints</A><BR>> to sort out some nomenclature. You probably want a dihedral<BR>> restraint with a strong force constant (though other approaches are<BR>>
possible). See relevant parts of chapters 4 and 5. Work by analogy<BR>> from the [dihedrals] and [position_restraints] sections in your<BR>> existing [moleculetype].<BR>> <BR>> Mark<BR>> <BR>> -----Inline Attachment Follows-----<BR>> <BR>> -- gmx-users mailing list <A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <<A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://us.mc1615.mail.yahoo.com/mc/compose?to=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<BR>> <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to <A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>> <<A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>>.<BR>> Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists"
target=_blank>http://www.gromacs.org/Support/Mailing_Lists</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 href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="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/Support/Mailing_Lists/Search"
target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR></DIV></BLOCKQUOTE></td></tr></table>