[gmx-users] Re: PMF of ligand transport

Thomas Schlesier schlesi at uni-mainz.de
Mon May 10 17:15:52 CEST 2010

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 
distance 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).


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 
generated umbrella sampling windows, you do not need to repeat the SMD. 
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 
 > > reference group should be the in the same direction of the channel(ie,
 > > at the intracellular end of the channel), so that if I use "position",
 > > 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 
then you're trying to hit a rapidly-moving target!  Always choose a 
static part of the structure in the direction you want to pull.


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