Hi Justin,<br>
<br>
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?<br>
<br>In order to further understand that "Distance " problem, May I ask one more question,( please ignore if its a stupid one..)<br>As Thomas suggested, = is the channel and x the dummy and l the ligand<br>
x l =====<br>
later time<br>
x ==l==<br>
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)<br><br>
And if we use a dummy particle, will the movement of that particle will also matter ? How can we fix that?<br> <br>Thank you.<br>Aswathy<br><br><div class="gmail_quote">On Mon, May 10, 2010 at 8:45 PM, Thomas Schlesier <span dir="ltr"><<a href="mailto:schlesi@uni-mainz.de">schlesi@uni-mainz.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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<br>
x l =====<br>
later time<br>
x ==l==<br>
Give the dummy no charge and zero lj-parameters and construt the position form the atoms at the entry of the channel.<br>
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).<br>
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.<br>
<br>
(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).<br>
<br>
Greetings<br><font color="#888888">
Thomas</font><div class="im"><br>
<br>
<br>
<br>
<br>
Aswathy wrote:<br>
> ><br>
> > Thank you very much for all replies.<br>
> ><br>
> > No w I just want to try SMd with geometry type as position . But one<br>
> > thing is still confusing me, ie; reference group.<br>
> ><br>
<br>
If you have already generated a suitable set of positions from which you have<br>
generated umbrella sampling windows, you do not need to repeat the SMD. Your<br>
problem was only related to the actual umbrella sampling itself.<br>
<br>
> > I have the ligand in the solvent (at the mouth of the<br>
> > channel(extracellular).) Now I want to pull this ligand to the<br>
> > intracellular solvent through the channel. My understanding is that the<br>
> > reference group should be the in the same direction of the channel(ie,<br>
> > at the intracellular end of the channel), so that if I use "position",<br>
> > the ligand should move towards the reference group (Please correct me if<br>
> > this wrong). i have only solvent at this end(end of the channel) . Can I<br>
> > set water molecules as reference point? or any molecule at this<br>
> > intracellular end is fine?<br>
> ><br>
<br>
In theory, you can set whatever you want, but if those water molecules diffuse,<br>
then you're trying to hit a rapidly-moving target! Always choose a relatively<br>
static part of the structure in the direction you want to pull.<br>
<br>
-Justin<br>
<br></div><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>