Hi all,
I noticed that with the same system (4x4x4nm of water), same boost parameters (both E and alpha), that NAMD and OpenMM give different temperatures. Specifically, the AMDIntegrator results in a temp of about 325K, whereas NAMD stays at 300K. Adding an Andersen thermostat (since i wasn't sure if the AMDIntegrator will regulate temperature by itself) doesn't help, if anything it introduces more temperature fluctuations. For NAMD I used langevin dynamics with a damping coefficient of 1/ps (same damping as the Andersen thermostat in openmm but I realise this is different thermostating).
Should boosting the total potential energy in aMD actually increase the temperature? And should this be rectified with a thermostat?
I have attached a picture of 100ps of aMD in either NAMD or OpenMM-with or without the Anderson thermostat.
Thanks for your time!
lewis
How best to regulate temperature during aMD?
- lewis martin
- Posts: 63
- Joined: Tue Mar 06, 2018 8:56 pm
How best to regulate temperature during aMD?
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- output.png (68.31 KiB) Viewed 246 times
- lewis martin
- Posts: 63
- Joined: Tue Mar 06, 2018 8:56 pm
Re: How best to regulate temperature during aMD?
HBonds, timestep, parameters/forcefield, cutoff are the same. Pressure control is necessarily different as NAMD has no montecarlo barostat.
NAMD, which I believe uses kcal/mol:
OpenMM:
and out of interest, the potential energy (namd output was adjusted to kj/mole). It is higher for OpenMM.
NAMD, which I believe uses kcal/mol:
Code: Select all
accelMD on
accelMDdihe off
accelMDE -19120.459
accelMDalpha 23.9006
accelMDFirstStep 0
accelMDOutFreq 1000
OpenMM:
Code: Select all
integrator = AMDIntegrator(0.001*picoseconds, 100*kilojoules/mole, -80000*kilojoules/mole)
...
totalPE = simulation.context.getState(getEnergy=True).getPotentialEnergy()
print("Potential energy: ", totalPE, "Boosted PE: ", integrator.getEffectiveEnergy(totalPE), "Boost only: ", integrator.getEffectiveEnergy(totalPE) - totalPE)
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- Peter Eastman
- Posts: 2583
- Joined: Thu Aug 09, 2007 1:25 pm
Re: How best to regulate temperature during aMD?
AMDIntegrator doesn't do any temperature regulation, so on its own it won't give a thermal distribution. AndersenThermostat ought to work fine with it. Can you provide a complete example (including input files) that reproduces the problem? Something that runs a simulation with AMDIntegrator and AndersenThermostat and has the temperature come out wrong.