[gmx-users] Error bar of order parameter

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 1/21/16 8:23 AM, m g wrote:
> Dear Justin,
>
>   I want to calculate the error bar for deuterium order parameter data for acyl
> chains of DPPC, for each carbons. I can calculate the Scd, i was learned it from
> your tutorial. but i don't know how can i get error bar for deuterium order
> parameter of each carbons. for example like this figure that attached. would you
> please help me?
>

I already told you how to do this.  Either compute these values from independent 
simulations, and average those values and obtain a standard deviation, or run 
gmx order with -b and -e and average over blocks of time and obtain a standard 
error.

-Justin

>
> On Thursday, January 21, 2016 4:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 1/21/16 8:03 AM, m g wrote:
>  > Dear Justin,
>  > in order to calculate the error bar for order parameter, i can't understand,
> which command exactly must be used? g_covar?g_anaeig? is it output of these
> commands?
>
> "Order parameter" is ambiguous.  What are you actually trying to do?  After
> reading about all available commands in the manual, what do you learn?
>
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

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

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

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