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

[Igaev, Maxim]

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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