[gmx-users] define statement in mdp file

[Justin Lemkul]

On Saturday, March 23, 2013, Shima Arasteh wrote:

> That's right.
> But I' d like to be sure about this fact that both restraints are applied.
> I see just 1 position restraints energy term in log file. Is just
> visualizing the trr file the only way of becoming sure that the headgroups
> and protein are restrained?
>
>
>
Either that or by measuring coordinates over time with g_traj. Effects of
restraints  should be fairly obvious when visualized.

And one more question is that, to eliminating the position restraints in
> MDRUN, is it supposed to reduce the force on atoms before mdrun gradually?
> Or it is ok to reduce it in MD step?
>
>
I am not sure I understand what you are asking.  It is usually sufficient
to simply turn off the restraints, but some people like to do a gradual
release. I usually do not find that necessary.

-Justin


> Thanks for your suggestions.
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu <javascript:;>>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com <javascript:;>>;
> Discussion list for GROMACS users <gmx-users at gromacs.org <javascript:;>>
> Cc:
> Sent: Saturday, March 23, 2013 10:37 PM
> Subject: Re: [gmx-users] define statement in mdp file
>
>
>
> On 3/23/13 8:59 AM, Shima Arasteh wrote:
> > Hi,
> >
> > I need to set position restraints on phosphorus head groups of lipids in
> addition of protein.
> >
> > In mdp file I added two lines:
> > define = -DPOSRES
> > define= -DPOSRES_LIPID
> >
> > But I get the error that multiple define assignments are not allowed. Is
> the "define= -DPOSRES_LIPID" is enough for both protein and headgroups?
> >
>
> Not likely, but that depends on the construction of your .top.  I will
> assume
> that each #define statement controls a separate topology, which is a good
> idea.
>
> The correct approach is to specify as many define statements as you like
> on one
> line (this is really just stolen from cpp):
>
> define = -DPOSRES -DPOSRES_LIPID
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>

-- 

========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================