CpHMD settings documentation - mms-fcul/CpHMD-container GitHub Wiki

... In the future will contain all the details and flags of the CpHMD settings with a brief description. ...

In the first block of this section you will be able to define several aspects of your CpHMD run.

  • GPU=1 - Turns on GPU simulations on our CpHMD run.
  • nCPU=8 - Defines the number of CPU to be used (default:8)
  • SysName="HEWL" - sets the name of our system as HEWL. (default:Protein)
  • SimTime=25 - Total time of the CpHMD production in ns (default 1 ns)
  • StartTime=0 - defines the starting time of our run in ns (default 0 ns)
  • ffID=G54a7pH - specifies the name of our force field, possible names are G54a7pH or CHARMM36pH or Amber14SBpH (default:G54a7pH)
  • pH=7.2 - sets the pH of our simulation (default 7.0)
  • temp=310.0 - sets the temperature of our system in Kelvin
  • sites="all 1N 4 10C" - defines the residues which are titrating. It is arguably one of the most important flags of the .settings file!

The sites definition will dictate which residues will be considered as titratable. Even if you changed them to the CpHMD compliant name, they may not be titrating if you don't include them in this list.

From this line, the CpHMD run will produce a .sites file with an indication of all titratable residues and their respective tautomers, so that the PB/MC cycle can define, at the simulation pH, which is the preferred state of each site.

Firstly, to construct this line, you need to define whether your termini are titrating. If they are uncapped they should always be titrating, hence they should be inserted into the sites as their residue number followed by N and C for which termini it is.

Secondly, you should define the residues in your structure that should be titrating. This can be done either through a string of residue numbers or through the flag all.

Caution

This flag will check your structure file for all residue names ending with a number and will consider them as titratable. It implies that only the CpHMD titratable amino acids end in a number due to their tautomers.

If, perchance, you have custom residues that end in a number, the all flag may raise problems.

After the sites definition comes the system specific definitions:

  • memb - will flag your system as a membranar system, so it should be set to 0

  • multiple_solutes - flags your system as composed of several undetached molecules which may interact, hence it is set to 0

  • include_itp - flags the system as having molecules treated as "include" in the topology, hence it is set to 0 in this tutorial too.

  • TOPin=""

  • GROin=""

  • NDXin="" -

  • CpHcontainer=""

Finally, this section ends by defining the mdrun parameters to perform the simulation. These should be adapted if your system requires a certain combination of flags to run the mdrun command of GROMACS.

  • mdruncpu="$GroDIR mdrun -nt $nCPU -pin auto " # Define which command should be used for parallel run
  • mdrungpu="$GroDIR mdrun -ntmpi 1 -ntomp $nCPU -gpu_id $GPUid -pin auto "
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