Dear Sir, I am new user in Gromacs. I am using Gromacs for protein-ligand complex. If I am not wrong MD simulation have three part. 1. Energy Minimization 2. Equilibration phase 3. Production phase
After EM minimization we run Equilibration using (NVT & NPT ensemble). I have little sily question in MD simulation. 1. In Protein-Ligand complex compulsory we have to run NVT & NPT ensemble ? 2 shall we run without NPT ensemble MD production phase ? 3. If we use both ensemble in production phase system might be NVPT like during production phase. 4. If we run only without NPT ensemble during production phase its affect MD simulation ? Thanks and Regards, -- ----------------------------------------------------------------- Haresh Ajani 09925522578
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