[gmx-users] gmx distance lipid bilayer

[xy21hb]

Dear all,

However, even if I choose B = C16 (last Carbon atom of sn-1 chain), it gives similar result.
Then I wonder how I could get the distance of my interest.

Thanks,

Yao









At 2015-09-30 23:20:28, "Justin Lemkul" <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
>
>==================================================
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.