[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
nasiri1355 at gmail.com
Sat Apr 17 18:33:04 CEST 2010
Thanks for the information.
Because of haven't satisfactory model from my co-solvent and I have to add
it randomly along with the solvent by genbox -ci -nmol.
the reason of this criteria relate to crash of system
(solute+co-solvent+solvent) in the first step of simulation, because small
distance between solute and co-solvents and co-solvents with themselves
cause to rise of pressure.
On Sat, Apr 17, 2010 at 6:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> rasoul nasiri wrote:
>> 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.
>> On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> 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 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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