I've been looking up how to confirm Pi-Pi interactions are happening in my simulations and if so what percentage they are occurring in the simulation. I found this: http://www.schrodinger.com/kb/1556 Which states:"Pi-pi stacking: A pi-pi interaction is defined as an interaction between two aromatic ...

Hi Peter, sorry for not being clear on this, i meant implicit water. In amber you only can create a Born implicit water model with sander during the simulation process, which is not included in the free ambertools12. What I need to do is load the inpcrd and prmtop files into OpenMM and have it run i...

Currently the only way I know how to simulate organic non-standard molecules is to use AMBER to make the inpcrd and prmtop with a box of explicit solvent.

Anyway to solvate them implicitly?

Thanks! -Jonathan

Doesn't seem like it is supported yet, any plans on supporting it in the future?

Thanks, Jonathan

I see what you mean, that obviously didn't work, I didn't think about rotation, silly me. I was looking into other programs solutions and they all seem the same, they just average the coordinates. This surprises me because of all this linear algebra/complex math used in the simulations it at least s...

I want to find the average structure of triphenylmethanol in water from a simulation I have done. Am I right to assume that the functions "ThreeParticleAverageSite()" and "TwoParticleAverageSite" are the ones I am looking for? What about atoms that are connected to four atoms? I've looked at 21.4 Vi...

There are 4 cl.exe's. I put all of their locations in PATH. I still get the same problem. Here is the error with echoed PATH and nvcc from console, everything seems to be recognized: Microsoft Windows [Version 6.1.7601] Copyright (c) 2009 Microsoft Corporation. All rights reserved. C:\Users\Unknown>...

Hi Peter,

I have VS 2010 and 2012 installed already.

Based on the error I thought maybe if i put the folder location of cl.exe in PATH it would work so i did "C:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\bin" but it still doesn't work.

Thanks.

I tested my newly installed OpenMM 5.0 by running testInstallation.py. I have a CUDA and OpenCl gpu, the OpenCl runs fine but CUDA gives an error. This is also a problem because when I run simulations it automatically runs the CUDA code, I do have CUDA installed. C:\sim>python 2cBenzene.py Traceback...

Yes was running 4.1, will be updating to 5.0 to see how it changes the output, thank you!