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

Merril Mathew mmathe01 at mail.bbk.ac.uk
Wed Mar 8 14:06:34 CET 2017


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.
Merril.

On 8 March 2017 at 12:56, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/8/17 7:52 AM, Merril Mathew wrote:
>
>> I am not sure what command to use to extract the X and Y box vector. is it
>> gmx energy -f md.edr -o .xvg?
>>
>
> Yes.
>
> and which option should I choose from the list?
>>
>>
> The ones I said before, (the aptly named) Box-X and Box-Y.
>
> -Justin
>
>
> On 8 Mar 2017 12:44 p.m., "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 3/8/17 7:28 AM, Merril Mathew wrote:
>>>
>>> I have a system that I simulated using GROMACS v5.0.4. The system is two
>>>> monolayers of lipid on each side of a box of water. I would like to know
>>>> if
>>>> there is a way to calculate area per lipid and monolayer thickness. I
>>>> read
>>>> that one can use gmx energy to find box size in X and Y and you divide
>>>> the
>>>> average time evolution box size( X*Y) by number of lipids.
>>>>
>>>> I used commmand:
>>>> gmx energy -f md.edr -s md.tpr -o box_vector.xvg
>>>>
>>>> What option should I select when prompted to get X and Y box
>>>> dimensions.?
>>>> How is the box vector calculated? I have noticed that the lipids pack
>>>> closely after simulation, that means the the area per lipid will be
>>>> smaller
>>>> than the initial configuration file. So does the box X and Y get smaller
>>>> as
>>>> well?
>>>>
>>>>
>>>> What you want are Box-X and Box-Y from the .edr file.  Then you can see
>>> the time series of how the box size changes.
>>>
>>> -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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> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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