[gmx-users] initial position?

[Justin Lemkul]

On 3/9/15 4:56 PM, Sadeghi, Ehsan wrote:
> Hi,
>
> I have simulated ionomer on Pt surface. I freezed  the Pt and put 5 ionomer polymers on top of it in a distance. Depends on the position of these polymers, it will get different results. Is it possible? For some cases, the ionomer backbone goes out of the box and interact with the neighbor molecules. How can I solve this problem?
>

This is why it is standard practice to run multiple simulations from different 
starting velocities or initial configurations.  Proper sampling is key.

-Justin

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

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

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