[gmx-users] Re: PMF of ligand transport

Aswathy ammasachu at gmail.com
Mon May 10 17:47:02 CEST 2010

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 more
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 already
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 uni-mainz.de>wrote:

> 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).
> 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 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
> 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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