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?
Rasoul On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul <[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 | (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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