[gmx-users] Re: PMF of ligand transport

Justin A. Lemkul jalemkul at vt.edu
Mon May 10 18:10:11 CEST 2010

Aswathy wrote:
> 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?

Yes.  The manner in which you generate the initial configurations on which you 
will conduct umbrella sampling is quite irrelevant.

> 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?

I think this is a rather complicated approach and you will probably spend a lot 
of unnecessary time troubleshooting it.  It might work, but you don't need it. 
Your problem is not with the SMD portion of the protocol.  Your problem is with 
umbrella sampling, which is a separate concept.


> Thank you.
> Aswathy
> On Mon, May 10, 2010 at 8:45 PM, Thomas Schlesier <schlesi at uni-mainz.de 
> <mailto: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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> Aswathy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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