Justin A. Lemkul wrote:
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.
I think I mis-read Thomas' post, but I'll agree with Chris that this approach is
still rather complicated and potentially error-prone. Using the appropriate
pull_geometry and a sensible reference group during umbrella sampling is all you
need to do.
-Justin
--
========================================
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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