[gmx-users] AFM-pulling

Alicia Lorenzo lorenzoalicia at yahoo.com.br
Mon Oct 28 19:10:45 CET 2002

Hi Justin.
Here we are again. We are trying to use the AFM pulling option for a while
As you suggested a previous mail a few months ago, we installed the updated
CVS version of gromacs (20.09.2002), and we found some weird things:

1) we performed several simulations with the following parameters:  
verbose = yes
runtype = afm
group_1 = Pull-atm  
reference_group = Chain-BC    
reftype = com
direction = 0.0 0.0 1.0
reverse = from_reference
pullrate = 0.0000005 
forceconstant = 1500

without constrains and a timestep = 0.0005 ps. In these conditions, the
spring position dislocated 0.01nm in 10 ps of simulation (as expected),
however the pulled_group (Pull-atm) has translated 14 nm by this time, which
is absurd. Either we are doing something wrong, or something is not working
on with the pull code.

2) We also tented to reproduce the same simulation in an effective medium (
epsilon-r = 78 ) but we couldn't do it without removing the center of mass
motion, because the 'nstcom' parameter does not accept other value than -1.
Free center of mass motion is absolutely necessary to perform the afm

We really hope you could dedicate some time to help us. We appreciate it a
lot. Thanks in advance,
Alicia and Ernesto
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