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. Aswathy On Mon, May 10, 2010 at 8:45 PM, Thomas Schlesier <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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy
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