[gmx-users] Re: Membrane Simulation

Giuseppe giuseppe.cimicata at studenti.unito.it
Wed Apr 24 10:49:07 CEST 2013

Dear Justin,

there were for sure some errors in the command, but even having solved them,
the protein still move during the optimization. What I noticed is that the
coordinates of the residues seems to decrease to zero and than "restart"
from a point out from the box. I mean, taking the first atom of the first
residue, after one EM the coordinates were:

1MET      N    1   6.100  15.879   0.231

after the second EM were

1MET      N    1   5.469  15.262   0.228

after the third EM were

1MET      N    1   4.870  14.676   0.225

and so on till the thirteenth EM in which the coordinates were

1MET      N    1   0.321  10.201   0.207

after this EM, protein moves off the membrane and the coordinates of the
first atom of the first residue become:

1MET      N    1  12.791   9.867   0.206

there is obviously something wrong with the x axis, but what?
The box vectors in this case were  6.23910   6.17970   6.91950 and the
complete editconf command was "editconf -f protein.gro -o protein_newbox.gro
-box 6.23910   6.17970   6.91950 -center 3.20920 2.72175 6.2 -rotate 145 -45
I also tried to use a larger box, which vectors were 12 12 12, and in this
case the complete editconf command was "editconf -f protein.gro -o
proetin.newbox.gro -box 12 12 12 -center 6 6 8.75 -rotate 145 -45 55" and to
decrease the scaling factor from 4 to 2, but it was useless. I'm sorry to
bother you so much, but I'm stucked with my project. Thank you so much.

Yours sincerely,  


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