[gmx-users] Position Restraints

[Justin A. Lemkul]

On 4/26/12 1:59 PM, Dariush Mohammadyani wrote:
> Thanks dear Justin.
> No, the protein is moving in right direction, but I am going to restrain any
> changing the position and then monitory these movements during MD run.
> I could see the Pos. Res. works in md.log file.

Then I don't understand what the problem is.  You'll have to describe what 
you're doing in greater detail.

-Justin

> Regards,
> Dariush
>
> On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:
>
>         Dear All,
>         I am using CG-MD using MARTINI forcefield. The system contains Protein
>         and lipid
>         bilayer. Although I used:
>         define = -DPOSRES
>         components in system were moving around and interact with each other.
>         Then, I
>         cannot do NVT or NPT equilibration.
>         Could you please let me know how can I control this kind of movements?
>
>
>     If molecules that should be restrained are moving inappropriately, then the
>     restraints are not being replied properly in the topology.  In the absence
>     of more substantial information, there's nothing else that can be said.
>
>     -Justin
>
>     --
>     ==============================__==========
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
========================================

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

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