[gmx-users] Change in the positon of structural Zinc and calcium ions during MD

2013-11-12 Thread Rama 

Hi Gromacs users,

I'm doing protein-Bilayer MD simulations. Enzyme contains structural zinc
and calcium ions during Energy minimization, NVT and NPT stage, ions are
changing there position even though I applied position restraints for the
atoms and ions.

Anyone could help me out.


Thanks

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Re: [gmx-users] Change in the positon of structural Zinc and calcium ions during MD

2013-11-12 Thread Justin Lemkul 



On 11/12/13 12:35 PM, Rama wrote:


Hi Gromacs users,

I'm doing protein-Bilayer MD simulations. Enzyme contains structural zinc
and calcium ions during Energy minimization, NVT and NPT stage, ions are
changing there position even though I applied position restraints for the
atoms and ions.

Anyone could help me out.



If the atoms are moving drastically, then the position restraints aren't taking 
effect, either because they haven't been invoked or they are insufficient. 
Without your full .mdp file and relevant topology snippets, there's no real way 
to know.  You can check the .log files, too - if there is not an energy 
component corresponding to position restraints, they haven't been activated.


-Justin

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==

Justin A. Lemkul, Ph.D.
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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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