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 <jalem...@vt.edu
<mailto:jalem...@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
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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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