[gmx-users] PMF of ligand transport

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue May 11 15:18:34 CEST 2010

It represents a difference in coordinate space. You'll get the most  
out of this list if you continue to try to solve your problems before  
posting and avoid submitting every question/problem that you hit upon  
under a continuously in-use title. Did you try it and look at you -px  
output file? I suggest that you do some tutorials. Also, set up a test  
system and pull two water molecules apart within a box of water and  
use VMD to see what happens. Then try a slightly more difficult test  
system... these are the types of things that worked for me.

pull_init1               = 0 0 -5
pull_init1               = 0 0 -4.9
pull_init1               = 0 0 -4.8
pull_init1               = 0 0 4.9
pull_init1               = 0 0 5

But it's up to you to determine the spacing. You need to get good  
overlap in order to be able to do WHAM. If you don't know how to  
figure that out then it's time for some reading.

Good luck,

-- original message --

Hi Chris,

Thank you very much for your detailed mail.

Now I have a doubt on this pull_init  parameter. i read your previous posts
regarding this, but still have a confusion.

My query is that for each configuration when I run umbrella sampling, will
this pull_init value needs to change?(I suppose so, if its true how?)

When it should be negative and positive?

Could you please explain this. Thanks for your valuable time

Thanks & Regards,

On Mon, May 10, 2010 at 9:55 PM, Chris Neale <chris.neale at utoronto.ca>wrote:

[Hide Quoted Text]
Pick a small collection of backbone atoms near the center of your channel
and use them as your reference group. Overcome the sign problem by optimal
selection of pull options (see below). pull_pbcatom values should not be
if you select your groups as I suggest -- otherwise be sure to understand
how they work.

pull                     = umbrella
pull_geometry            = position
pull_dim                 = N N Y
pull_start               = no
pull_nstxout             = 250
pull_nstfout             = 250
pull_ngroups             = 1
pull_group0              = MY_SELECTION_OF_BACKBONE_ATOMS
pull_pbcatom0            = 0
pull_group1              = LIGAND
pull_pbcatom1            = 0
pull_init1               = 0 0 THISDIST
pull_rate1               = 0
pull_k1                  = 500.0
pull_vec1                = 0 0 0


-- original message --

I think Justin meant that you have various positions of the ligand in the
channel (from the SMD), so you don't need to make a new run to determine new
positions in the channel. You need only new umbrella sampling simulations.

Yep, the movement of the particle will also matter, because if the particle
moves much on the z-axis, the distance between the particle and the ligand
will change. So you would want the particle fixed relative to the channel.
Two ideas:
Place the particle above the entrance of the channel. Pick three atoms from
the entrance of the channel and determine the distance between the atoms and
the particle. Then use distance_restraints or constraints with a
'bondlength' equal to the measured distance. If everything goes right the
particle would stay where you placed it, since it does not interact with the
enviroment it should not really influence your simulation (only through the
constraints or distance_restraints).
I don't now how big your system is, but it would probably be a good idea to
make a short test simulation, to look if the particle changes the system
But it's only an idea, i hope other people comment it.


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