Hi, A system I'm working with has a C-terminal proline on one of the chains. I noticed in an old github post (https://github.com/pandegroup/pdbfixer/issues/112), that the type for HA needed to be changed from 55 to 54. Even after that correction, however, I notice the following issue: The multipole ...

We downloaded and compiled the source from github yesterday and recompiled it, and I submitted two test jobs. One of them died with the same CUDA 700 error I have mentioned in my first post in this thread, and the other died with the following error: Traceback (most recent call last): File "equilibr...

Hi Dr. Eastman, The input files can be found here https://www.dropbox.com/sh/ytttz7ju0y8h2w1/AABl_PhEqjmB_EWSdjEL6th2a?dl=0 This simulation died with the CUDA error before the first restart file was written, i.e. <10ps. However, I'm not sure if this is deterministic and if it would die at the exact ...

Hi Dr. Eastman, I'm still seeing this problem. I tried with different proteins, as well as water boxes of different sizes. However, I'm still seeing this error. And it is stochastic, i.e. if I restart the exact same simulation, the error occurs at a different point in the trajectory. In addition, so...

Hi Dr. Eastman,

I've tried compiling the latest source version from the github. I'm still seeing the exact same problem. Also, this problem is quite random, i.e. it occurs in some trajectories and not in others.

Saurabh

I'm not sure of the exact subversion, but we had pulled the source from github in early July.

Saurabh

Hi, I'm running a version of OpenMM 7 compiled from source from the github version. I've been running it for a few months, without any noticeable issues. However, the current set of simulations I'm trying to run give me the following error: Traceback (most recent call last): File "equilibrate_npt.py...

Hi Dr. Eastman,

Is there an automated code/script available somewhere, which can convert a TINKER prm file directly into an OpenMM compatible xml file, for any new parameters developed for AMOEBA?

Thanks!

Hi Dr. Eastman,

You're right. The problem was because I was running with python 2.6.6. I changed to python 2.7.9 and the make completed successfully.

Thank you.

Hi Dr. Eastman, I'm trying to compile the latest github version of OpenMM on a linux cluster and getting the following error on executing make [ 97%] Creating OpenMM Python swig input files... Traceback (most recent call last): File "/home/sbelsare/software/OpenMM/build_openmm/python/src/swig_doxyge...