I need to perform some MD calculations and then trajectories of some small molecules analyzed.

What I have is

  1. protein
  2. cofactor (FAD)
  3. small molecule (either single O2 molecule or single Chlorine atom)
  4. crystallographic waters

The software I can access is Gromacs (with yum install)

I have tried and tried to get this to run (for 6 months perhaps), to no avail. The input files located on the web do not work on the version of Gromacs provided by the yum install command.

Is there a kind soul somewhere that would have suitable input files that would do all the steps described below and who'd be willing to pass them on to me?

What needs to be done is:

  1. add waters to the crystallographic waters in order to fill a box of suitable size
  2. generate parameter and topology files for each component separately
  3. merge these into global parameter and topology files for the system
  4. run initial Energy Minimization
  5. run M.D. simulations
  6. analyze the trajectories of the small molecules.
  • 4
    $\begingroup$ Hi @fred.vellieux, what was the error that you got from gromacs? What was the version of gromacs and what type of coordinate file are you using for your biomolecules? $\endgroup$
    – mykd
    Aug 4, 2020 at 11:36
  • 2
    $\begingroup$ What force field are we talking about? The procedure varies greatly depending on that $\endgroup$
    – Godzilla
    Aug 4, 2020 at 11:47
  • $\begingroup$ I removed reference to Maestro since it seems that was not usable anyways (due to license cost) $\endgroup$
    – Cody Aldaz
    Aug 4, 2020 at 17:10
  • 2
    $\begingroup$ This question is too general. I suggest you take a look and follow the GROMACS tutorials at mdtutorials.com they cover many different things with detail. $\endgroup$
    – Ivan
    Aug 7, 2020 at 23:02
  • 1
    $\begingroup$ I’m voting to close this question because the two questions in the comments have not been answered and the user has not been online since early August (1 week since opening their account). $\endgroup$ Sep 26, 2020 at 6:05


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