[gmx-users] Deuterium Order Parameter Calculations

[Justin Lemkul]

On 5/30/17 7:16 PM, Sanim Rahman wrote:
> Hello everyone,
> 
> I have a question about calculating Deuterium Order Parameters using
> g_order. Is it common to get unrealistic values for Scd if you have not run
> the simulation long enough (over 25 ns?)? I ran the calculations after
> equilibration on a POPC bilayer just to experiment with the command and I
> received "NaN" values for two of my carbons for my calculations on Sn1.
> 

This means something is wrong with your inputs, likely incorrectly specified 
index groups.

-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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