Implicit Solvent

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    • Dec 5th, 2022 at 11:03 am #25849

      obasekia
      Participant

      Good day all, is it possible to use GamD with implicit solvent with genesis?

    • Dec 5th, 2022 at 1:01 pm #25850

      tmori
      Moderator

      Yes, it is possible.
      First, please prepare the control file for GaMD.
      Then, in the case of GBSA, please add “implicit_solvent = GBSA” in the [ENERGY] section.
      For details, see the User manual Chapter 6 or Tutorial 2022 Chapter 8.1.

      Bests,
      Takaharu Mori

    • Dec 6th, 2022 at 6:17 am #25851

      obasekia
      Participant

      Thanks that means i can use atdyn rather than spdyn for the simulation of GaMD?

    • Dec 6th, 2022 at 10:52 am #25853

      tmori
      Moderator

      Please see the User manual p.28 Table 3.1.
      GaMD should be available in not only atdyn but also spdyn.
      But, implicit solvent is only available in atdyn.

      Bests,
      Takaharu Mori

    • Dec 6th, 2022 at 3:11 pm #25855

      obasekia
      Participant

      Thanks, i will check it out. my other question is, how do you check for convergence in GaMD?

    • Dec 6th, 2022 at 3:21 pm #25856

      tmori
      Moderator

      Sorry, I am not an expert on GaMD…
      I will await comments from someone else,
      but I think it would be good to read some papers on GaMD.

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