I am running a typical MD simulation of a protein ligand complex in NAMD using OPLS-AA/M force field and its parameter. I want to study the change in conformation of the receptor during MD simulation. Here I have attached my conf file for running the MD simulation of the complex in NAMD. Can anyone please check the conf file and give me any suggestion.
Thanks
For such calculation, better to run two individual simulations, one is ligand-bound system (holo) and second is ligand-free system (apo), then try to compare their trajectory frames.
For such calculation, better to run two individual simulations, one is ligand-bound system (holo) and second is ligand-free system (apo), then try to compare their trajectory frames.
If you are running explicit solvent simulations, it is recommended that during the equilibration stage the complex (protein+ligand), or at least all heavy atoms, to be fixed at their reference structure. For this you have to use 'constraint' simulation and set up 'on' the constraint in the configuration NAMD file. The equilibration protocol include:
a) Structure minimization;
b) Heating/cooling solvent at NVT ensemble;
c) Harmonic restraints on complex, which are slowly removed, until the complete system become flexible.
Then, you are ready for normal NPT (or NVT) long run simulations, where all system is flexible.
In addition, from your NAMD configuration file I noticed that
cellOrigin 64.35704040527344 31.88634490966797 181.7159423828125
It seems too 'off' the center of mass (or geometry) of your system. You may want to check this, using for example 'measure center' command in VMD.
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