[gmx-users] AFM pulling of two groups

[Berk Hess]

>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?

That should be ok.
>From the information you sent me I can't see what could be the problem.

>
>To use the free energy code, am I obliged to supply the structure of the
>state B (in my case the network after shrinkage )?

Yes.

>I can foresee only part of it (the junction zones). The remaining part of
>the system is what i'm trying to obtain.

But why not use pressure coupling to shrink the system?

Berk.

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