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

Peter C. Lai pcl at uab.edu
Fri Apr 8 05:58:05 CEST 2011

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               |

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