[gmx-users] tilt angle for POPC

Justin Lemkul jalemkul at vt.edu
Fri Jan 19 13:56:16 CET 2018



On 1/18/18 2:44 PM, Mohsen Ramezanpour wrote:
> I did more tests and here are the conclusions for the pick mentioned
> earlier.
>
> The pick appears when the -binw gets smaller and smaller.
> For the default value of gangle (which is 1), one cannot detect such a pick
> and you will get a normal distribution.
> Even for a -binw of 0.1 everything looks fine.
> However, for -binw of lower than 0.1, e.g. 0.5 or so, the picks appear.
>
> Well, is this a problem with POPC simulation, POPC topology, POPC
> parameters, the algorithm behind gangle, or it is what is really happening
> and we do not detect it due to the NOT enough Small value of -binw in the
> histogram?

It's up to the user to determine what a suitable bin width is for the 
data being collected. The default option is a fairly fine binning so 
having to go much smaller likely reflects the fact that your particular 
data are very narrowly distributed.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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