[gmx-users] question about martini coarse-grained

mohammad agha mra_bu at yahoo.com
Wed Sep 21 14:49:21 CEST 2011

Dear Gromacs Users,
>I want to simulate 150 surfactant molecules in the water by MARTINI Coarse-Grained force field, and I have several questions please:
>1- I defined 2 groups in index.ndx file named "surfactants"
          and "w_ion_ wf" that second group is consist of water,
          antifreeze water and ions. Is my definition good for index
>2- For add the water and antifreeze water to my system, I use
          the "gro" file of water (consist of 400 W) in MARTINI site for
          both of them, but in the second one (antifreeze water), I
          changed W to WF in this file. Is it right?
>3- When I minimize my system, in the first steps of
          minimization, potential is a large positive number and when
          converge to Fmax, it is a negative large number from 10e+05,
          but when I work with gromos96 force field, the first steps of
          minimization are negative. Is it a problem about my
          minimization with MARTINI Coarse-Grained? and what do I do
>4- For equilibrium step in simulation, I want that restraint
          my surfactant molecules, so, I made a "posre.itp" for
          surfactant molecules by "genrestr" program, but when I run a
          "pr.mdp" for 20ns to density adjustment, my surfactant
          molecules are assembled and is made micelle, while I want to
          remain in random place in primary state!!! what do I do?
>Please help me.
>Best Regards
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