[gmx-users] Deuterium Order Parameter Calculations

[Sanim Rahman]

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?

Regards,
Sanim Rahman



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
>> 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
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