[gmx-users] AFM pulling of two groups

[Ester Chiessi]

>Pulling is always between the reference group and one or more other groups.
>If you want to pull between two group you need to supply the reference group
>and group_1.
>
>You did not supply the force constants for the afm pulling (afm_k1 and
>afm_k2).
>Maybe afm_k2=0.

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

; AFM OPTIONS
; Pull rates in nm/ps
afm_rate1                = 0.00001
afm_rate2                = 0.00001
afm_rate3                = 0
afm_rate4                = 0
; Force constants in kJ/(mol*nm^2)
afm_k1                   = 100
afm_k2                   = 100
afm_k3                   = 0
afm_k4                   = 0
; Directions
afm_dir1                 = 1 1 0
afm_dir2                 = 0 -1 1
afm_dir3                 = 0.0 0.0 1.0
afm_dir4                 = 0.0 0.0 1.0
; Initial spring positions
afm_init1                = -8.92024 -8.98945        0.111007
afm_init2                = -0.0257715      8.9218  -8.95815
afm_init3                = 0.0 0.0 0.0
afm_init4                = 0.0 0.0 0.0

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?

To use the free energy code, am I obliged to supply the structure of the
state B (in my case the network after shrinkage )?
I can foresee only part of it (the junction zones). The remaining part of
the system is what i'm trying to obtain.

Thanks for your attention

Ester




Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Università di Roma Tor Vergata
Via della Ricerca Scientifica
00133 Roma
tel. +39 06 72594462
fax  +39 06 72594328
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm