[gmx-users] Position Restraints with NVT and NPT

[Justin Lemkul]

On 4/20/14, 9:05 PM, zanemarkson wrote:
> Dear All GMX Users
>
> I have some questions about doing NPT equilibration while keeping my protein
> (or small molecule) fixed. I know there have been a lot of discussion about
> this topic but after reading them I am still confused. So could anyone
> please give me some clear answer or insight about the following questions?
> Thank you in advance!!!
>
> 1) By including the pores.itp into my topology file, am I really position
> restraining the chosen atoms? I did a NVT equilibration with a pores.itp
> included in my topology file and "define = -DPOSRES" written in my .mdp
> file. After the mdrun was done, I used g_traj to check the coordinates of
> those "fixed" atoms. However, instead of seeing non-changed coordinates, I
> can see the Cartesian coordinates of those "fixed" atoms changed. The
> magnitude of changing is in the order of 0.001nm.
>

First, realize that "restraining" and "fixing" are not equivalent terms.  A 
position restraint is merely a biasing potential that disfavors movement; it 
does not prevent it.  A change of 0.001 nm is insignificant and indicates that 
the restraints are working effectively as well as you can expect.

> 2) So if including pores.itp is not a good option for fixing chosen atoms,
> what is the best way to do it. What will the .mdp file look like? What I am
> really trying to do here is simply just to equilibrate my solvent molecule
> while  keeping my protein (or small molecule ) fixed.
>

If you want to fix the atoms, use freezegrps, but note that freezing is a 
significant perturbation that is really only needed in the most extreme cases. 
Normal equilibration protocols only call for restraints.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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