[gmx-users] switch/shift function

Cristian Danciulescu danciulescu at dwi.rwth-aachen.de
Mon Jul 14 15:22:01 CEST 2003

Dear gromacs users,
I tried to use the switch function for Coulomb and LJ interactions for 
simulating a small peptide (30 res.) in a-helical conformation (in water, 
at 300 K) and I noticed that the helix collapses after few ps (less than 20 
ps). Using the twin-range cut-off method, the helix is stable during the 
simulation (t> 500 ps).
I used the following parameters:
rlist = 1.0 nm (I could not set rlist larger than rcoulomb or rvdw as 
recomended in the manual v.3.0)
rcoulomb = 1.4 nm
rcoulomb_switch = 1.2 nm
rvdw = 1.4 nm
rvdw_switch = 1.2 nm

rlist = 1.0 nm
rcoulomb = 1.4 nm
rvdw = 1.0 nm
Has someone encountered the same problem (the instability of the protein) 
using the switch function or could explain the reason for this behaviour?
Thank you.

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