[gmx-users] Re: Membrane Simulation
jalemkul at vt.edu
Wed Apr 24 14:20:25 CEST 2013
On 4/24/13 4:49 AM, Giuseppe wrote:
> 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
The only way that this is possible is if your protein is much larger than your
box. Note that the y-coordinate of the N atom of Met1 begins at nearly 16 nm,
which is more than twice the box vector in the y-dimension. I suspect that your
protein is ill-suited to being positioned within a box of these dimensions.
Note too that centering on z=6.2 almost assuredly places your protein outside
the box if the z-dimension is 6.9195 nm.
If there are further problems, separate the rotation and placement steps. I
don't recall off-hand which operation is done first, but this can be a source of
complication. Rotate your configuration first, then position it in a second step.
> 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.
A box size of 12 is still incompatible with the coordinates shown above.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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