[gmx-users] Membrane

[Justin Lemkul]

On 3/1/16 3:02 PM, Abbas Ebadi wrote:
> Dear Gromacs Users,
> I'm trying to simulate the permeation of Dendrimer into a DPPC membrane.
> Whenever I use constraint in my simulations, they interact together easily
> without any problem. However, when I remove constraint, my system collapse
> entirely. How can I avoid this problem? thanks for your time.

Probably because your time step is too large to be used in the absence of 
constraints.  But that's just a guess because you haven't provided much useful 
information, .mdp settings, etc.

-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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