From: Mike Makowski (mmakowsk_at_uci.edu)
Date: Sun Aug 10 2014 - 18:05:21 CDT
I suppose I should provide a bit more information:
The last line of output prior to meeting any errors is:
USING GEOMETRIC MEAN TO COMBINE L-J SIGMA PARAMETERS
(note that it said arithmetic mean before invoking vdwGeometricSigma).
Following this there are a series of lines with "ERROR" before proceeding
and attempting a single simulation step with energies outputting a maximum
value.
I hope this is clear.
Michael Makowski
University of California, Irvine
Department of Chemistry,
Chemical and Material Physics,
Irvine, CA 92617
Cell: 267 588 9865
Office: 949 824 5776
On Sun, Aug 10, 2014 at 3:44 PM, Mike Makowski <mmakowsk_at_uci.edu> wrote:
> 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,
> Mike
>
> 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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