[gmx-users] Error

[Justin Lemkul]

On 11/4/14 2:55 PM, asasa qsqs wrote:
> Dear Justin Lemkul,
> Is the position restrain very important for NVT and NPT steps? I have an ionic liquid that made of 2 fragment, cation and anion, but cation fragment didn't restrain at the NVT and NPT steps. I did production posre.itp for cation and anion .gro file and included to topology file but just anion was restrained,what must i do?
>

The fact that you attempted to restrain a molecule and it was not restrained is 
a product of either (1) incorrect define keyword in the .mdp or (2) topology 
construction problem.  If you want to restrain the molecule, you need to figure 
out which item failed.

As to whether or not you need restraints, I'd say probably not in this case. 
For a small molecule that comprises part of the solution, restraints don't serve 
much of a purpose.  For something larger, like a protein, restraints serve to 
avoid initial "kicks" from random velocities that may distort the structure. 
For a small molecule, the need for restraints is probably minimal.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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