[gmx-users] define statement in mdp file

[Shima Arasteh]

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?


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?

Thanks for your suggestions.

 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
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

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