[gmx-users] pulling

aherz alexander.herz at mytum.de
Fri Jul 31 12:13:07 CEST 2009


I appear to have serious trouble understanding how to set up the pulling

I have many configurations of a protein partially adsorbed to a froozen
surface (the configs differ
in the amount of the protein that has been desorbed).
Now I want the pulling to keep the distance of the desorbed end of the
protein to the surface using the harmonic pot.
Now the documentation is not very clear how this all works so I ran
several experiments to figure it out but I failed.
I use the following options:

pull                     = umbrella
pull_geometry            = distance
pull_dim                 = N N Y
pull_nstxout             = 1000
pull_nstfout             = 1000
pull_ngroups             = 1
pull_group0              = GLD
pull_group1              = ASN
pull_vec1                = 0.0 0.0 0.0
pull_init1               =   5.27778
pull_rate1               = 0.0
pull_k1                  = 100

where gld is the surface and asn is the end residue of the protein and
pull_init1 is set to the desired COM distance of the two
groups (gld is froozen). I use the same settings for all runs, only
changing pull_init1 to get the desired distance.
Now for some reason using this setup either pulls the ASN end of the
protein completely onto the surface or very far away from it depending
on the value I use for pull_init1.
So the distance between what and what shall I put for pull_init1? What
else is wrong?


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