Aswathy wrote:
On Mon, May 17, 2010 at 12:14 PM, Aswathy <[email protected]
<mailto:[email protected]>> wrote:
Hi,
I tried to calculate PMF for the ligand transport using
pull_geometry=position.
Let me explain you what I did so far,
I picked a small collection of backbone atoms nearly from the centre
of the channel.My SMD was displacing the ligand from extracellular
to intracellular.
I checked the pullx file for getting the window spacing (pull_init ).
Initial structure is at =7.61
Centre of the channel(reference) =8.20
Last displacement is at =8.91
Therfore I selected pul_init as 0.6, 0.5, 0.4 ,....0....-0.4,-0.5,-0.6
For example, the first frame(at 7.61) was sampled using the
following parameters,
pull = umbrella
pull_geometry = position
pull_dim = N N Y
pull_start = no
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0 = U_ref
pull_pbcatom0 = 0
pull_group1 = r_C1
pull_pbcatom1 = 0
pull_init1 = 0 0 0.6
pull_k1 = 1000
pull_rate1 = 0
pull_vec1 = 0 0 0
The problem is that the ligand undergoes a displacement to wrong
direction during sampling. My idea was pull_k1 = 1000 is the force
to keep ligand in one place where it get sampled?
I want to add some more points to this. I agree that as I am using the
"Position" , it should be displaced to the position of reference. But my
worry is that, when i visualize this trajectory, within the first two or
three frames, ligand get displaced. As per my u understanding, we need
to sample well at the same position to get the PMF at that point.(Is it
so?) in that case, the sudden drop from the initial position will cause
any problem in the PMF?
There is nothing wrong. Your ligand will move around; that's what MD does. As
long as the reference distance between your ligand and bilayer remains correct
there is no problem. The umbrella potential is a harmonic restraining force,
allowing for some deviation in position such that the ligand about the sampling
window. If there is some drastic change in position such that this reference
distance is no longer conserved, then you have a problem. But certainly this is
not what is happening within only a few frames.
-Justin
Is there anything wrong that I am doing?
any suggestions will be appreciated.
-Aswathy
On Tue, May 11, 2010 at 11:15 AM, Aswathy <[email protected]
<mailto:[email protected]>> wrote:
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,
Aswathy
On Mon, May 10, 2010 at 9:55 PM, Chris Neale
<[email protected] <mailto:[email protected]>> 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.
; COM PULLING
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 [email protected]
<mailto:[email protected]>
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
[email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Aswathy
--
Aswathy
--
Aswathy
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
