[gmx-users] membedded.gro from g_membed has broken molecules (fix periodicity?)

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Apr 8 06:07:08 CEST 2011

Hi Peter,

No, you don't need to fix molecules prior to MD.
Fixing them is also not that hard. Build the .tpr, just using the
structure with molecules broken, and then use it as reference
structure to trjconv, with -pbc mol. That will fix the molecules based
on the distances between bonded atoms, which should turn out the way
you want.

Hope it helps,


On Fri, Apr 8, 2011 at 5:58 AM, Peter C. Lai <pcl at uab.edu> wrote:
> The output of g_membed is membedded.gro which appears to have broken lipids
> at the box boundaries, making the box "smooth" (as if g_membed did not fix
> the periodicity of the final frame) when visualized in VMD. How do I fix the
> periodicity for visualization - I cannot use trjconv -s membed.tpr because
> it complains about the missing atoms from the original tpr, as g_membed
> deletes molecules on the fly after calculating the overlaps...
> Perhaps more importantly, should I try to make the membedded.gro whole
> before using it as the input coordinate file for the subsequent equilibration
> md? The g_membed paper does not mention this...
> Thanks from your neighborhood gromacs noob.
> --
> ===============================================================
> Peter C. Lai                 | University of Alabama-Birmingham
> Programmer/Analyst           | BEC 257
> Genetics, Div. of Research   | 1150 10th Avenue South
> pcl at uab.edu                  | Birmingham AL 35294-4461
> (205) 690-0808               |
> ===============================================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list