Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On Mon, Mar 18, 2013 at 8:24 AM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> Yes, I overcome the last problems and I could see the pos.rest energy term
> in my log file.
> In order to create the itp files to include in top file, I opened the gro
> file which I entered as an input in my mdrun command. How might I check
> this issue that all the atoms in itp groups are  involved in position
> restraints? Is there any solutions to check it?
>
>
The input coordinate file doesn't tell you anything. Load the trajectory
and watch it. If atoms are moving that shouldn't be, you have a problem.
Inspect the position restraint .itp file to see which atoms it covers, and
cross-reference those with the chain topologies to make sure the atoms you
think are being restrained actually are.

-Justin

-- 

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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

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