[gmx-users] Deuterium Order Parameter Calculations
sanimr at mail.usf.edu
Wed May 31 17:35:09 CEST 2017
Thank you Justin,
That makes much more sense. I was able to fix the error. I have one more
question that is out of topic from the original question. Is there a guide
that informs the user on what index groups should be made for each type of
analysis? I am also trying to use gmx_potential to do electrostatic
potential on a membrane solvated in KCl. If I want to do this, what index
group would I use?
On Tue, May 30, 2017 at 8:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users