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Questions related from Munazzah Fatima Ansari
What happens in the simulation, if we have replicas at different temperature. Furthermore, one replica in this set never returns to its initial temperature. How we will get the probability...
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Hi, I am learning about the H-REMD (Hamiltonian Replica Exchange Molecular Dynamics) method. I am concerning about how to prepare different topology files for creating different replicas. Is there...
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Hi, I am using AMBER Software for Molecular Dynamics Simulation. I was trying to minimize the system with SHAKE algorithm, but the minimization calculation has always ended up with "RESTARTED DUE...
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Hi, I 'm new to MD simulation. I was performing replica exchange method from Amber tutorial. In the tutorial developers uses Amber16 and they get the remd.mdcrd* files in human readable format...
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Hello, I am studying a system with the method GaMD in Amber. Can I calculate collective variables like ALPHARMSD, BETARMSD, etc. from the Plumed? And then reweight with the GaMD reweighting methods?
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