[gmx-users] gmx distance lipid bilayer

[Repic Matej]

As said, you are not measuring what you presumably want. As I understand,
you should be measuring the distance between the com of P atoms from the
same _monolayer_ and the com of all lipids (or all P atoms of the
bilayer). This way, the first com will be in the middle of the plane
formed by the P atoms in one monolayer, and the other com will be in the
middle of the plane at the interface between top and bottom bilayers. This
distance should be similar to the length of the acyl chain.

It is customary to measure the membrane thickness in lipid simulations as
P-P distance, so I suggest you make top and bottom P groups in a ndx file
and measure the distance between the two centers of mass. This value can
also be compared to experiment to validate the simulation.

Best,

------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------







On 9/30/15, 17:20, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Justin Lemkul"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jalemkul at vt.edu> wrote:

>
>
>On 9/30/15 11:17 AM, xy21hb wrote:
>> Dear all,
>>
>> I am using gmx distance to calculate the distance between the center of
>>mass (c.o.m.) of the phosphorous group (PO4, 5 atoms)
>> and the c.o.m. of the lipid bilayer system in Justin's tutorial (a
>>typical lipid DPPC bilayer system) by issuing, as shown on GROMACS
>>website for gmx distance,
>>
>> gmx distance -n index.ndx -select 'com of group "A" plus com of group
>>"B"' -oxyz -oall -s md.tpr -f md.trr
>>
>> where A = Phsphorous B = System.
>>
>> The distance should be about the chain length of the lipid, so ~ 20 A
>>
>> However, it gives ~ 0.1 nm. I just wonder why it is like that.
>>
>
>Because your assumption is wrong.  The bilayer is centered in the box, so
>the 
>COM distance between the center of the system and the center of the P
>atoms is 
>usually about the same position, so you get a value that is nearly zero.
>
>-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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