[gmx-users] Re: Membrane Simulation
giuseppe.cimicata at studenti.unito.it
Wed Apr 24 10:49:07 CEST 2013
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.
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