[gmx-users] Re: PMF of ligand transport

Thomas Schlesier schlesi at uni-mainz.de
Mon May 10 18:13:41 CEST 2010

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.


 >Hi Justin,
 >I am sorry, i dint understand this point "Your problem was only 
related >to
 >the actual umbrella sampling itself." ? You meant I just want to repeat
 >umbrella sampling only?
 >In order to further understand that "Distance " problem, May I ask one 
 >question,( please ignore if its a stupid one..)
 >As Thomas suggested, = is the channel and x the dummy and l the ligand
 >x l =====
 >later time
 >x   ==l==
 >If this is the case, then  there wont be sign problem with "distance",
 >right???  (Once again forgive me if I am wrong, because I know you 
 >put your maximum effort to make me understand this thing)
 > And if we use a dummy particle, will the movement  of that particle >will
 >also matter ? How can we fix that?
 >Thank you.
 >On Mon, May 10, 2010 at 8:45 PM, Thomas Schlesier <schlesi at 
 > Would it be possible to use a dummy particle near the entrance of the
 > channel? = is the channel and x the dummy and l the ligand
 > x l =====
 > later time
 > x   ==l==
 > Give the dummy no charge and zero lj-parameters and construt the position
 > form the atoms at the entry of the channel.
 > I think it will be important that the dummy is farther away from the
 > channel then your ligand, else you will get problem with the distance
 > geometry (because the distance changes the sign).
 > The other important thing is that the box is long enough that the 
 > between the dummy and your ligand is always smaller then half the box
 > vector, or else the distance goes wrong.
 > (My first idea was to use the entrance area of the channel as the
 > reference, but then there would be the problems with the sign-changing of
 > the distance -> so the idea with the dummy particle).
 > Greetings
 > Thomas
 > Aswathy wrote:
 > > >
 > > > Thank you very much for all replies.
 > > >
 > > > No w I just want to try SMd with geometry type as position . But one
 > > > thing is still confusing me, ie; reference group.
 > > >
 > If you have already generated a suitable set of positions from which you
 > have
 > generated umbrella sampling windows, you do not need to repeat the SMD.
 >  Your
 > problem was only related to the actual umbrella sampling itself.
 > > >  I have the ligand in the solvent (at the mouth of the
 > > > channel(extracellular).) Now I want to pull this ligand to the
 > > > intracellular solvent through the channel. My understanding is 
that the
 > > > reference group should be the in the same direction of the 
 > > > at the intracellular end of the channel), so that if I use 
 > > > the ligand should move towards the reference group (Please correct me
 > if
 > > > this wrong). i have only solvent at this end(end of the channel) 
. Can
 > I
 > > > set water molecules as reference point? or any molecule at this
 > > > intracellular end is fine?
 > > >
 > In theory, you can set whatever you want, but if those water molecules
 > diffuse,
 > then you're trying to hit a rapidly-moving target!  Always choose a
 > relatively
 > static part of the structure in the direction you want to pull.
 > -Justin
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