[gmx-users] PMF of ligand transport

Aswathy ammasachu at gmail.com
Tue May 11 07:45:45 CEST 2010

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:

> 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
> important
> 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
> Chris.
> -- 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
> behavior.
> But it's only an idea, i hope other people comment it.
> Greetings
> Thomas
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100511/5ff5602e/attachment.html>

More information about the gromacs.org_gmx-users mailing list