[gmx-users] creating an "infinite" filament with editconf

Igaev, Maxim maxim.igaev at mpibpc.mpg.de
Wed Dec 9 22:21:15 CET 2015

Hi Alexey,

thanks for the hint. Should I disable the pressure coupling completely or how do I disable it in the direction of the filament (z in my case)?

Currently, my mdp file for production runs looks like this (in a simplified way):

integrator = md
nsteps = 10000000
dt = 0.002
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 0.95
vdw-type = cut-off
rvdw = 0.95
tcoupl = v-rescale
tc-grps = Protein non-Protein
tau-t = 0.5 0.5
ref-t = 300 300
pcoupl = parrinello-rahman
pcoupltype = semiisotropic
tau-p = 2.0 2.0
compressibility = 4.5e-5 4.5e-5
ref-p = 1.0 1.0
cutoff-scheme = Verlet
nstxtcout = 5000
nstenergy = 5000
constraints = all-bonds
constraint-algorithm = LINCS
pbc = xyz
periodic-molecules = yes

I would be really grateful if you could point out the relevant part. I presume this should be "pcoupletype", shouldn't it?

Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se]" im Auftrag von "Alexey Shvetsov [alexxy at omrb.pnpi.spb.ru]
Gesendet: Mittwoch, 9. Dezember 2015 22:06
An: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Betreff: Re: [gmx-users] creating an "infinite" filament with editconf


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:alexxyum at gmail.com
mailto:alexxy at omrb.pnpi.spb.ru
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