Hi Lee-Ping,

I was using the documentation for FB ver 1.3. The part about interaction energies is under section 3.3 "setting up the targets" on page 10.

Thanks for your help!

Andrish

Hi Lee-Ping, I was able to reproduce your diffusion values for iamoeba using the method you described. I wanted to clarify some things about the QM calculations: 1. For the range of ion vdW radii (-0.4 through +0.4) do you mean just offsetting the sigma value for the ion vdW in the amoeba ff to (sig...

I think it has to do with how PME is calculated in a multi-gpu setup. If I change my cutoff type to 'NoCutoff' or 'CutoffNonPeriodic', then the simulation proceeds normally using both gpus (albeit slower than a single gpu). The amoeba forcefield is only compatible with PME which is why the error can...

Hi Peter, Yes, I was originally working with the CUDA platform and got the error, which prompted me to check OpenCL as well. The error is compounded when using amoeba vs amber, or other non-polarizable forcefields. I am using a small water box of 512 molecules, and the salient parts of my script are...

Hi, I am testing a dual gpu setup on openmm 6.2 using the precompiled binaries for linux64. I am using 2 stock-clocked GTX 970 gpus on pcie x16 slots. Any simulation I run with CUDA(6.5) or OpenCL, including the ones in the example folder can run fine when selecting either gpu0 or gpu1, however, whe...

Hi Lee-Ping, Thanks for your help thus far. I have one more question as to the information required by the qdata file. If I am optimizing the ion parameters: vdw-epsilon, vdw-sigma, polarizability, and thole, then how many snapshots would I need from the qm run? Also what would you suggest in terms ...

Hi Lee-Ping, I was able to get a better density approximation by removing the constraints. I am trying to reproduce the diffusion constant by the method you suggested. I wanted to know whether it's fine to pull the velocities from getVelocities in my NPT system and calling setVelocities without corr...

Thanks for the quick response

I will remove restraints and let you know how it went.

Andrish

Thanks Lee-Ping, Yes that is what I meant to say regarding the parameters/targets. I am trying to replicate your results for the density and diffusion constant for iamoeba using openmm 6.2 and the CUDA platform with a stock-clocked gtx 970. For the diffusion constant I get 2.90 E-5 cm^2/s, where I s...

Hi Lee-Ping, In terms of editing the iamoeba.xml file to include initial parameters for say an Na+ ion, could I just copy the parameters from the amoeba ff for Na+ and add them under the appropriate directives: <AtomTypes>, <Residues> <Amoeba VdwForce> <Multipole> and <Polarize> ? I could then selec...