[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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