Running NAMD via GROMACS topology

From: Mike Makowski (
Date: Sun Aug 10 2014 - 17:44:35 CDT

Hello NAMD community,

I'm attempting to run simulations using GROMACS topology and coordinate
inputs. The coordinate input reads properly but I'm generating errors when
reading in the Lennard-Jones parameters and the simulation crashes with
atoms moving at very high velocities. Considering that GROMACS generally
performs the geometric mean (unlike NAMD's arithmetic mean) to calculate
molecular parameters, I tried applying the vdwGeometricSigma but it's not
making a difference. I was also concerned that the units were incompatible
so I modified the input for values in terms of angstroms but that also
didn't seem to make a difference. Might there be anyone who knows how NAMD
reads in GROMACS inputs and may provide more information than can be found
on the NAMD website? Thanks in advance!

Best Regards,

Michael Makowski
University of California, Irvine
Department of Chemistry,
Chemical and Material Physics,
Irvine, CA 92617
Cell: 267 588 9865
Office: 949 824 5776

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