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

muhammad tahir ayub tahirgp0 at gmail.com
Thu Sep 3 13:56:36 CEST 2015

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
rlist            1.2 to 0
rvdw          1.2 to 0
rcoloumb   1.2 to 0
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

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*

*Junior Research Fellow*

*H.E.J Research Institute of Chemistry*

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