[gmx-users] any alternative methods?

[Justin Lemkul]

On 8/21/12 2:25 AM, Mark Abraham wrote:
> On 21/08/2012 4:00 PM, Albert wrote:
>> Dear:
>>
>>   I am going to calculate the area/lipids for my membane system and I found
>> that GridMAT for area/lipids calculation is not that reliable since I
>> calculate by XY/(0.5 lipids number) for the pure well equilbirated POPC lipids
>> system, my values is 67 which is close to experimental data but GridMAT give
>> me something 72.....
>>   I am just wondering is there any alternative methods?
>
> Since that calculation is one of the main purposes of GridMAT, I'd suspect
> you're comparing two different quantities, or not calculating one correctly.
>

We did several calculations on pure lipid bilayers in our initial testing of 
GridMAT-MD and always found it to agree very well with other methods, so this 
outcome is very surprising to me.  In the absence of more information that would 
be necessary for troubleshooting, I do not see a reason for the discrepancy.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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