[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

[rasoul nasiri]

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.

Rasoul

.


On Sat, Apr 17, 2010 at 6:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <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
>>
>>
>>    --     ========================================
>>
>>    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
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at 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-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>
>>    Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100417/249bfdd0/attachment.html>