Hi Steve,
I also use the pull code and would be very interested to more fully
understand the problem that you are experiencing. However, I don't
generally modify any code myself, and therefore have no use for your
private system. What I would be eager to receive is your
POPC-buckyball system with a small instruction on how I might detect
the difference between 4.0.3 and 4.0.99 behaviour.
chris.neale |at| utoronto.ca
Chris.
-- original message --
Hi,
The permeants in my bilayer system are improperly pulled in calculations
using all versions of Gromacs 4.0.x including the VERSION
4.0.99_development_20090120. Since, due to restrictions, I can not
provide the topology file for my system to bugzilla, I constructed a
similar prototypical system using Prof. Tieleman's POPC bilayer
coordinates and field parameters. A buckyball permenat doped in the
center of this system did indeed react similarly in a 4.0.3 calculation
with an improper pull away from the equilibrated 3.3.1 constraint force
coordinates. It was heartening to see that this problem was fixed for
that system, by using VERSION 4.0.99_development_20090120.
Unfortunately, again the problem remained for my actual system, even
with use of the newest version of code.
Since the cylinder option is now operational, I have a viable
work-around for this problem. I am quite appreciative of the attention
that this issue has received. If there is continued interest, and a
willingness for an engineer to receive the topology file in a less
public forum than bugzilla, I believe we could proceed with the
debugging process.
Thank you,
Steve Fiedler
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