Hi!
So far I have been preparing my MD systems for NAMD using Modeller and CHARMM-GUI. I am thinking about switching to Schrodinger suite of programs. To perform MD I am using a supercomputing center not supporting Desmond. Is it possible to (without any complicated modifications) use systems (homology models with ligands, lipid memebranes etc) build in Maestro in NAMD?
So far Desmond is quite great for MD work with Maestro, tomy knewlodge transformation would require little changes like removing atoms with PDB atom name pseu if generated in NAMD.
To run MD simulations in NAMD you will need three files:
1) Topology file;
2) Coordinates file;
3) Force field parameters file.
If the force field you use, either using Desmond or NAMD, is the same, then the results should be compatible. Of course there are some other details on the setup, such as type of thermostat you use and numerical integrators. But, I think both use the standard one, such as Nose-Hoover chain of thermostats for equilibrating the temperature.
You can open your ".pdb" file of your system with mastro and go to Tasks select the simulation you want e.g: Desmond Molecular dynamics or Jaguar ..etc. and in the new window configure your simulation and type: Run
If you are preparing the system in CHARMM-GUI it has option for Desmond with CHARMM force field. If you are preparing the system in Schrodinger Suite ( Force Field mainly OPLS) You have to save it as PDB and export to VEGAzz software (windows based GUI) .In Vega ZZ software you can create the topology and coordinates files for NAMD'
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics