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

[Justin Lemkul]

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

==================================================