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

Vitaly V. Chaban vvchaban at gmail.com
Mon Dec 7 13:16:09 CET 2015

Perhaps, it is technically easier to freeze the boundary atoms along the
periodic direction.

On Mon, Dec 7, 2015 at 9:26 AM, David van der Spoel <spoel at xray.bmc.uu.se>

> 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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