gmx3 at hotmail.com
Fri Jul 31 12:18:00 CEST 2009
I hope you are using 4.0.5, I fixed several bug in the pull code for older 4.0 versions.
The problems you are seing could be due to pbc.
Do you have pbc in Z, and what is the height of your box?
A safer setup is:
pull_geometry = direction
pull_vec1 = 0 0 1
But they should give the same answers if you do not have pbc issues.
> Date: Fri, 31 Jul 2009 12:13:07 +0200
> From: alexander.herz at mytum.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pulling
> 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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