Hi!
I previosly tryed to create an infinite filaments for RecA proteins. The
trick is not to apply pressure coupling in direction of filament access.
Igaev, Maxim писал 07-12-2015 13:54:
Dear Gromacs Users,
I have a protein dimer and would like to make an "infinite" filament
out of it in z direction by using periodic boundary conditions and
editconf. What I've done so far is
a) I've generated a topology for the dimer via
pdb2gmx -f dimer.pdb -o dim.gro -p dim.top -i dim.itp -water tip3p
(force field was chosen interactively)
b) and created a periodic box by using editconf
editconf -f dim.gro -o dim_box.gro -bt triclinic -box 13.4 9.4 8.6
-center 6.7 4.7 4.3
If I understand editconf correctly, it is supposed to create a
periodic box of sizes 13.4 x 9.4 x 8.6 and place the dimer's center of
mass to (6.7, 4.7, 4.3) in this box. The size "8.6 nm" in z direction
is the priodicity of my dimer, which means that the dimer doesn't fit
completely into the box; some parts are sticking out. But this is
needed to establish the periodicity.
When I try to equilibrate my system after sufficient energy
minimization I get an error like "X particles communicated to PME node
Y are more than a cell length out of the domain decomposition cell of
their charge group", which means that my system is blowing up and I
probably have a bad starting structure. I then checked whether my
dimer has some steric clashes and it was fine. I could equilibrate my
dimer in a normal water box (isolated dimer) and the simulation was
just fine.
I wonder if I did something wrong during the editconf step. Should I
wrap my dimer into the box after editconf so that I have no parts
sticking out of the box?
In NAMD, a similar approach worked well - I just took my dimer and
surrounded it by waters to have a box of sizes 13.4 x 9.4 x 8.6 and
applied PBC to it. But how to do the same in GROMACS?
Thank you in advance for your help!
Cheers,
Maxim
--
Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexx...@gmail.com
mailto:ale...@omrb.pnpi.spb.ru
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