External force applied but not effective

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Peter Eastman
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Re: External force applied but not effective

Post by Peter Eastman » Tue Apr 16, 2019 1:58 pm

You're still missing the PSF and CRD files. Can you just put everything in a single zip file that I can download, then tell me exactly what command to run to reproduce what you're doing?

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Ross Gunderson
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Re: External force applied but not effective

Post by Ross Gunderson » Wed Apr 17, 2019 7:34 am

Hey Peter,

Due to size, I will give you a link to the zip file. It is approximately 300 MB uncompressed.
https://drive.google.com/file/d/1rkuv-i ... sp=sharing

When I run the simulation, I run it through the scrip "slurm.sh", which runs on a GPU at a national lab. In that file you will find the call to OpenMM and the files given at call.

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Peter Eastman
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Re: External force applied but not effective

Post by Peter Eastman » Thu Apr 18, 2019 3:03 pm

Got it, thanks. What am I supposed to be seeing? Your PSF file is just a box of water. I verified that the CustomExternalForce is applying an identical force of (1, 0, 0) to every atom. Is that not what you expect? There's nothing in here that would produce any kind of difference with respect to height. And since the CMMotionRemover forces the mean velocity to be 0, a constant force applied to every atom basically has no effect.

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Ross Gunderson
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Re: External force applied but not effective

Post by Ross Gunderson » Fri Apr 19, 2019 6:42 am

Ah! The last part of your statement is what I was looking for. We were expecting to see a difference in velocity due to the applied force. But if the simulation is removing the CM motion, it would set it back to zero?

Many thanks! Sorry this took so long for me to get you what you needed.

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Peter Eastman
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Re: External force applied but not effective

Post by Peter Eastman » Fri Apr 19, 2019 9:41 am

But if the simulation is removing the CM motion, it would set it back to zero?
Yes, but only because you're applying an identical force to every atom. You previously described a membrane simulation and said you were applying a force to the water but not the membrane. In that case you should see the water moving one way and the membrane moving the other way. CMMotionRemover removes center of mass motion, but it still lets different parts of the system move relative to each other.

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Ross Gunderson
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Re: External force applied but not effective

Post by Ross Gunderson » Fri Apr 19, 2019 12:16 pm

That makes sense! Thanks for the thorough explanation and helping me find the source of the problem. I will remove the CM motion remover and try again!

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