[gmx-users] Re: position / distance restraint involving more than one molecule

[Dr. Vitaly Chaban]

Thank you, Justin. Supplying desired conf.gro is indeed a wise solution.


On Tue, Nov 13, 2012 at 4:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/13/12 9:59 AM, Dr. Vitaly Chaban wrote:
>>
>> Dear All -
>>
>> Is it possible in the current gromacs to apply position restraints NOT
>> in respect to the initial position of the particle, but in respect to
>> an explicitly specified position within a box, such as (0,0,0) or
>> (LBOX/2, LBOX/2, LBOX/2).
>>
>> Perhaps, some wise tricks exist...
>>
>
> Indeed, per grompp -h:
>
> "When using position restraints a file with restraint coordinates can be
> supplied with -r, otherwise restraining will be done with respect to the
> conformation from the -c option."
>
> -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
>
> ========================================