rasoul nasiri wrote:
Hi,
Thanks for the replies.
Since I want to increase distance among co-solvents with themselves and
with solutes, i must firstly fill the co-solvents along solutes and
solvents after that i remove solvent, finally by edittconf -translate
the co-solvents uniformally is distributed in the appropriate distances.
Is it OK?
Why bother adding solvent if you're just going to remove it? Here's what I
would do:
1. Position solutes in the box with editconf -center
2. Add co-solvents (with a large value of -vdwd, I suppose)
3. Add solvent
I don't fully grasp why the initial position of the co-solvents matters so
precisely; you may have a hard time satisfying all of the simultaneous distance
requirements. Everything is just going to diffuse around anyway during MD.
Maybe you have some reason I'm not thinking of, but it's a potentially
complicated problem to build.
-Justin
Rasoul
On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Justin A. Lemkul wrote:
rasoul nasiri wrote:
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance
between solutes in simulation box before MD simulation. How
can I do it?
You can't. If you know you need a certain distance, that should
be part of your planning :) I suppose you could run a pulling
simulation to separate your two species, but that requires
substantially more work (and setup considerations) than the two
or three quick editconf commands to properly build the system.
Correction: you can use editconf -translate with appropriate index
groups to separate your solutes. This will also imply that you
haven't added solvent, which is the same thing as positioning the
two solutes appropriately in the first place (with editconf -center,
as I posted before).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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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