[gmx-users] orires energy terms

[Berk Hess]

Hi,

"Orient.-Rest." is the potential energy of the restraints (in kJ/mol).
"Ori.-R.-RMSD" is the RMS deviation of the orientations in units of your orientation
observable input.

Berk.

> 
> There is another question that could possibly be answered by Berk: I 
> often use his Orientation Restraints algorithm implemented in Gromacs. 
> While all results are fine and most of the analysis parameters of an 
> RDC- driven run are clear to me, I am not sure of the meaning of the 
> g_energy output "Orient.-Rest." and "Ori.-R.-RMSD". Are these analysis 
> parameters some kind of energy terms like the
> restraining potential or is the output given in Hertz and what do they 
> actually mean?
> 
> Thanks in advance for any help,
> 
> Andreas
> 
> 
> 
> Xavier Periole wrote:
> 
> > On Wed, 12 Mar 2008 12:24:02 +0100
> >  Berk Hess <gmx3 at hotmail.com> wrote:
> >
> >> Hi,
> >>
> >> Did you make your DMSO molecule completely rigid?
> >>
> > Should we really worry about such a difference in density?
> > (1095-1108)/1095=0.012
> >
> > How precise is the value reported? Did you estimate the error
> > by using different sections of the trajectory?
> >
> >> Berk.
> >>
> >>> Date: Wed, 12 Mar 2008 12:18:08 +0100
> >>> From: andreas.frank at ch.tum.de
> >>> To: gmx-users at gromacs.org
> >>> Subject: [gmx-users] DMSO G53a6 FF in Gromacs
> >>>
> >>> Dear Gromacs Users,
> >>>
> >>> I simulated the preequilibrated box of DMSO that is located in the 
> >>> Gromacs Force Field Distribution with the G53a6 Gromos FF parameters 
> >>> (adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)). 
> >>> After temperature equilibration I performed a NPT run but in 
> >>> contrast to the reported density of 1095 kg m-3 I always get values 
> >>> around 1108 kg m-3. I used berendsen pressure coupling as well as 
> >>> reaction field for treating long-range interactions with 0.8 / 1.4 
> >>> cut-offs.
> >>> I looked through the  Gromacs archive but couldnt find an answer for 
> >>> this problem. Has anyone an idea what could be the reason for this 
> >>> result?
> >>>
> >>> Thanks for any comments!
> >>>
> >>> Best regards,
> >>>
> >>> Andreas
> >>> -- 
> >>>
> >>> _______________________________________________
> >>> gmx-users mailing list    gmx-users at gromacs.org
> >>> http://www.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-request at gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> >> _________________________________________________________________
> >> Express yourself instantly with MSN Messenger! Download today it's FREE!
> >> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> >
> >
> > -----------------------------------------------------
> > XAvier Periole - PhD
> >
> > NMR & Molecular Dynamics Group
> > University of Groningen
> > The Netherlands
> > http://md.chem.rug.nl/~periole
> > -----------------------------------------------------
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> -- 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080312/7661ecbd/attachment.html>