[gmx-users] No error but no of lipids are different in confout.gro and system_inflate.gro

[Justin Lemkul]

On 9/3/15 7:56 AM, muhammad tahir ayub wrote:
> Dear Gromacs experts
>
> I am running membrane tutorial KALP15 in DPPC
> I have run the command
>
> mdrun -v -s em.tpr
>
> by which confout.gro was created which contained 128 DPPC moleucles inspite
> of changing the cutoff values in the minim.mdp md.log and mdout from 1.2 to
> 0
> rlist            1.2 to 0
> rvdw          1.2 to 0
> rcoloumb   1.2 to 0

Don't do this.  The cutoffs affect the physics; the only "cutoff" you should be 
changing here in the context of this procedure is the one used by InflateGRO for 
determining atomic overlap.

> I have also changed the cutoff values of only minim.mdp file
> but the result was confout.gro with 128 DPPC molecules, the
> system_inflate.gro file contains the 126 DPPC molecules
>
> when running the following command
>
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
>
> system_shrink1.gro contained 128 DPPC molecues
>

Then you've confused your file names by relying on default names.  If you 
initially inflated the system and got 126 DPPC (which is correct) there is no 
way that they magically get added back.

-Justin

> Area per protein: 0 nm^2
> Area per lipid: 0.583197761890625 nm^2
>
> Area per protein, upper half: 0 nm^2
> Area per lipid, upper leaflet : 0.583197761890625 nm^2
>
> Area per protein, lower half: 0 nm^2
> Area per lipid, lower leaflet : 0.583197761890625 nm^2
>
> I don't know where i am making problem
> Today complete day was served to get rid of this problem but this problem
> was not solved
>
> Thanks in advance
>
> *Muhammad Tahir*
> *Ayub*
>
> *Junior Research Fellow*
>
> *H.E.J Research Institute of Chemistry*
>

-- 
==================================================

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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