[gmx-users] Position Restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 26 20:47:16 CEST 2012
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.
> 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 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>
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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