[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 |
More information about the gromacs.org_gmx-users