[gmx-users] AFM pulling of two groups

Justin MacCallum jlmaccal at ucalgary.ca
Thu Jan 20 17:53:42 CET 2005

> Thanks for your reply.
> I verified the force constants for the afm pulling were both specified:

It looks like your ppa file is correct

> I'm working with a single large molecule (a polymer network) and the groups
> are parts of it. I built the network by assemblying different chains and
> jointing them by chemical bonds. Now I should shrink the system to the
> correct density and the pull facilities seem very promising.
> I use no constraints and a time step of 0.5 fs. Is it a problem to have
> groups part of the same molecule, with the 3.2.1 version?

I don't believe that it should be. I believe there is a bug which
presents a problem for pulling more than one group. I believe that this
his been fixed in the CVS version but I'm not positive. Its in the file
pullio.c if I remember correctly. If you search the developer mailing
list you should be able to find the required patch.


Justin MacCallum	PhD Student
Biocomputing Lab	Department of Biological Sciences
University of Calgary	http://moose.bio.ucalgary.ca
jlmaccal at ucalgary.ca	(403) 220-2264

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