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Can not use all cpus for one walker ABF method #8
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"logger": {
"frequency": 100,
"output_file": "cvs.dat",
"cvs": [0, 3]
} If you have any further questions, please let us know! |
Thank you very much for your suggestions. |
Dear Sir,
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"output_file": ["cvs_w0.dat", "cvs_w1.dat"]
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Thank you. |
I was trying a 2 walker simulation of ADP in solvent. After some time the job was killed, displaying the following error.
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Dear Sir,
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I'm afraid that these error messages aren't enough to help diagnose your problem. If there is more output surrounding these error messages, please copy as much as is relevant. Or if your issue is reproducible, you can attach the files needed to run your simulation so that the development team can try to reproduce your issue. This way, we can try to debug whatever is happening in this system. |
Dear Sir,
to
and added
to the .json file.
I am getting the following error:
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Dear Sir,
I am trying to run a one walker ABF on ADP system. My system is consisting of 1 socket, 4 cores per socket and 2 threads per core (1x4x2=8 CPUs). But when I run the job using "ssages 1walker.json" it uses only 3 CPUs (from top command %CPU). How can I use all CPUs to get good performance?
When I run the same job on a system consisting of 2 sockets, 6 cores per socket, 2 threads per core (2x6x2=24 CPUs) it gives the following error:
2 walker job is running perfectly fine with full efficiency with the command
mpirun -np 24 2walker.json
on this system.How to know the convergence of ABF method using this software? Does the simulation terminate automatically after it converges? If not, how to extend the simulation using this software?
How to extract the structures of the free energy minima from the trajectory? As we do not have any file which provides collective variable values to be printed along the simulation time, which is helpful to get the frame numbers in extracting the structures corresponding to particular minimum. Like COLVAR file in PLUMED Software.
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