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