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

Igaev, Maxim maxim.igaev at mpibpc.mpg.de
Mon Dec 7 14:06:32 CET 2015

Thanks David, thanks Vitaly for your answers.

@Vitaly: I also thought of this but the number of boundary atoms is too high. I'm afraid of introducing too many artifacts through the freezing.

@David: the default -dd option of mdrun says that gromacs will guess the optimal size of the domains. The same for -npme. Do you mean I should just vary the size of the domains to find an optimal decomposition grid? I rather thought that the parts of my dimer that are not in the box after editconf and genbox should be "put"/"wraped" back into the box somehow...

Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se]" im Auftrag von "David van der Spoel [spoel at xray.bmc.uu.se]
Gesendet: Montag, 7. Dezember 2015 12:26
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] creating an "infinite" filament with editconf

On 07/12/15 11:54, Igaev, Maxim wrote:
> 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.
You're doing everything right, but will have to tweak the mdrun command
line settings to control the parallellization, in particular -dd and -npme
> 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

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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