On Sat, Apr 6, 2013 at 5:37 PM, Juliette N. <[email protected]> wrote:
> Dear all, > > I need to add 100 molecules of a second solvent to my polymer. I do this in > two solvation steps as below: > > genbox -cp Solute.gro -ci Solvent1.gro -o solute-solvent1.gro -nmol 500 > > genbox -cp solute-solvent1.gro -ci Solvent2.gro -o > solute-solvent1-solvent2.gro > -nmol 100 > > 1- Is this the correct of adding two solvents to a solute? or This has to > be done in one step. > > It is not possible to use the -ci -nmol mechanism with multiple molecules in one step. > 2- Does the box size (last line in gro) of solvent affect the final box > size of the solute-solvent1.gro? I mean do I need to keep size of > Solvent1.gro > or Solvent2.gro as small as possible to avoid huge box for > solute-solvent1.gro > or solute-solvent1-solvent2.gro? > > Did your approach work? The box vectors in the inserted coordinate file are irrelevant. > 3- In mdp file do I have to assign the uniform solution temperature to each > component or that is sufficient to have tc-grps = System ? > > Technically, coupling the system together is the only correct way to treat thermostats. In practice, the exact implementation depends on the chosen thermostat algorithm. See extensive discussions in the list archive on this topic. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/Support/Mailing_Lists/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/Support/Mailing_Lists
