[gmx-users] Re: restraints between two molecules

[lq z]

Thanks, Justin. How to use "index groups"? Do I do it in .mdp file or use
some program in tools/?

Luke


*Justin A. Lemkul* jalemkul at vt.edu
<gmx-users%40gromacs.org?Subject=%5Bgmx-users%5D%20restraints%20between%20two%20molecules&In-Reply-To=CAJLK-9VYnde6D7SxY_eOLbQbTkoQmrTSn%3Dme2a%2Bdj4Q1h%3DsKEg%40mail.gmail.com>
*Fri Dec 2 18:04:37 CET 2011*

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lq z wrote:
>* Dear GMXers,*>* *>* I can apply harmonic bond, angle, and dihedral restraints between two *>* molecules (3 atoms on one, and one atom on the other one). If yes, how *>* to set it up in the topology file?*>* *
They have to be in the same [moleculetype].

>* Question 2: Can I apply distance restraint between mass center of some *>* atoms in one molecule and ONE ATOM in the other molecule?*>* *
Yes, with the pull code and suitable index groups.

>* Question 3: Can those restraints be lambda (in alchemical free energy *>* simulation) dependent?*>* *
Yes, see the manual.

-Justin

>* You may have known what I'm trying to do: Change one molecule to dummy, *>* so I need restrain it at dummy state while no restraint is wanted at *>* real state.*>* *>* Thanks,*>* Luke*>* *
-- 
========================================

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

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



On Fri, Dec 2, 2011 at 11:59 AM, lq z <lqz.fsu at gmail.com> wrote:

> Dear GMXers,
>
> I can apply harmonic bond, angle, and dihedral restraints between two
> molecules (3 atoms on one, and one atom on the other one). If yes, how to
> set it up in the topology file?
>
> Question 2: Can I apply distance restraint between mass center of some
> atoms in one molecule and ONE ATOM in the other molecule?
>
> Question 3: Can those restraints be lambda (in alchemical free energy
> simulation) dependent?
>
> You may have known what I'm trying to do: Change one molecule to dummy, so
> I need restrain it at dummy state while no restraint is wanted at real
> state.
>
> Thanks,
> Luke
>
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