[gmx-users] AFM pulling of two groups
ester.chiessi at uniroma2.it
Thu Jan 20 11:54:41 CET 2005
>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
>You did not supply the force constants for the afm pulling (afm_k1 and
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
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
Dipartimento di Scienze e Tecnologie Chimiche
Università di Roma Tor Vergata
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