[gmx-users] Re: Re: angle restraints

[Maarten Wolf]

David,

Thanks for your reply.

I am currently using 3.3.1 code. 

I am increase the force, to be able to calculate the free energy
required of introducing the angle restraints in the system. I use small
force increments each run, using a delta_lambda of 0. 

Decreasing or increasing in my view only changes the sign of the
overall graph, but it should not allow dG/dl to cross zero.

Thanks,
Maarten

> > From: "David Mobley" <dmobley at gmail.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Thu, 11 May 2006 09:34:28 -0700
> Subject: Re: [gmx-users] angle restraints
> 
> Maarten,
> 
> What version of the code are you using? There was a bug in the angle
> restraints code until 3.3.1 (or 3.3 cvs) which caused angle
> restraints
> to turn off gradually as a function of lambda in free energy
> calculations, if I remember correctly. (See bugzilla for details:
> http://bugzilla.gromacs.org/show_bug.cgi?id=43).
> 
> However, I'm not sure that relates to the problem you're describing,
> but it probably does, depending on the version you are using.
> 
> What exactly are you changing in the free energy calculation? Are you
> changing the angle restraint as a function of lambda? If so, which
> way
> are you changing it? Decreasing or increasing restraints?
> 
> David
> 
> 
> 
> On 5/11/06, Maarten Wolf <maarten_wolf at yahoo.co.uk> wrote:
> > Dear users,
> >
> > I have a small system with a number of small peptides. I want to
> > constraint the angle between the N-term to C-term vectors of
> different
> > peptides. This works well, but if I do a FEP calculation the dG/dl
> > becomes smaller than zero at some point.
> > I expected it to be at least allways greater than zero (zero in the
> > limit that the restraint does not have to do anything), since a
> force
> > has to be aplied to restraint the angles.
> > Can anybody explain where I am going wrong?
> >
> > Thanks
> > Maarten
> >
> > Send instant messages to your online friends
> http://uk.messenger.yahoo.com
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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
> 


MvG Maarten

******************************************************
**  Work Adress         Julianalaan 136             **       
**                      2628 BL Delft               **
**                      Netherlands                 **
**                      +31(0)15-2789382            **
******************************************************


		
___________________________________________________________ 
Switch an email account to Yahoo! Mail, you could win FIFA World Cup tickets. http://uk.mail.yahoo.com