Re: [gmx-users] Deuterium Order Parameter Calculations

[Justin Lemkul]

On 5/31/17 11:35 AM, Sanim Rahman wrote:

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?



The group(s) you supply to any analysis tool depend on what you want to do. 
Sorry, no one-size-fits all guide exists, nor should it.  Scientific inquiry 
rarely fits into a neat little box.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [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  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
>
> --
> ==
>
> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [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

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] Deuterium Order Parameter Calculations

[Sanim Rahman]

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.

I will truly appreciate your response and assistance.

Regards,

Sanim Rahman

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Research Assistant, Bhethanabotla-Frisina Neural Plasmonics Stimulation
Group

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