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 <[email protected]> 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 <[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 >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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