[gmx-users] Calculating area per lipid and monolayer thickness

[Merril Mathew]

thanks Justin.

On 8 Mar 2017 13:09, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 3/8/17 8:06 AM, Merril Mathew wrote:
>
>> I dont know what I am doing wrong. There is no Box-X or Box-Y when
>> prompted. These are the list I get:
>> -----------------------------------------------------------------
>>   1  Angle            2  Proper-Dih.      3  Ryckaert-Bell.   4
>> Improper-Dih.
>>   5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8
>> Disper.-corr.
>>   9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12
>> Kinetic-En.
>>  13  Total-Energy    14  Conserved-En.   15  Temperature     16
>> Pres.-DC
>>  17  Pressure        18  Constr.-rmsd    19  Vir-XX          20
>> Vir-XY
>>  21  Vir-XZ          22  Vir-YX          23  Vir-YY          24
>> Vir-YZ
>>  25  Vir-ZX          26  Vir-ZY          27  Vir-ZZ          28
>> Pres-XX
>>  29  Pres-XY         30  Pres-XZ         31  Pres-YX         32
>> Pres-YY
>>  33  Pres-YZ         34  Pres-ZX         35  Pres-ZY         36
>> Pres-ZZ
>>  37  #Surf*SurfTen   38  T-DPOPG_OPO     39  T-SOL_Ion
>>
>> 38 and 39 are the coupling groups I used.
>>
>
> If there is no option to select box vectors, then your simulation was NVT
> and by definition the box vectors don't vary and your membrane area is
> constant.
>
> -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 | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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