Hi Peter, I have been using the RPMD Integrator and I found that if you run the simulation for more than a couple of ns, the center of mass motion of the system drifts. This happens if you are using the CUDA platform and the precision is set to single or mixed. Interestingly, if you specify only 1 c...

You were right, the precision of the coordinates was too low (only 3 decimal places). I used a configuration from Gromacs with more precision and the energies are in great agreement. Thanks for the help.

Hi, I have been doing tests between Gromacs and OpenMM. I minimized a peptide using Gromacs (charmm36 forcefield). The energies that gromacs gave at the end of the minimization is Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.67638e+01 2.25811e+01 1.28747e+02 2.69536e+00 -8.16862e...

There were a couple of things that I have simulated with negative pressure. One I was looking at the behaviour of liquid water at negative pressures to see at which temperatures it would begin to cavitate. Another is related to the compression and subsequent decompression of solids and glasses. In t...

Hi Peter, I installed the newer version of OpenMM and I got a weird error. The MC barostat now gives an error if you try to set the pressure to be negative. With the older OpenMM version (7.4.0) there was no issue with setting the pressure to be negative. I do want to add that I have run simulations...

Hi, I have some files from gromacs (the topology and gro file) that I wanted to run using OpenMM. The system contains a protein and some water molecules. I can run the system with OpenMM, however I wanted to change the water model that I am using to 'qtip4pf'. I have the forcefield xml file for this...

Hi, I'm trying to implement the ring-polymer contraction scheme (RPC), however I've run into some strange problems. I can't get the speed up of ~6 when using 32 beads per ring-polymer. I'm using a flexible forcefield model of water (q-TIP4P/F), which contains bonded and nonbonded forces. I first set...

The energy minimizer won't work for a PIMD system then and I don't want to minimize the classical system. Is there a way around this?

Hi, Can you use the energy minimizer for a PIMD configuration in OpenMM. So I have a configuration where I saved the positions of all the replicas. I then want to perform an energy minimizer to see what the new positions and minimized energy will be. I can do this for a classical system (i.e. using ...

Hi, I wanted to know what type of thermostat is the RPMD plugin using. Is it a local or a global thermostat? The manual isn't clear about which type of thermostat it is. The manual mentions the paper "Efficient stochastic thermostatting of path integral molecular dynamics", however the paper itself ...