Hello All,
I am using MMPBSA to calculate ligand binding energies for a variety of analytes with various amino acid based micellar systems. I would like to be able to plot ligand binding energy as a function of simulation time. When running MMPBSA calculations does it calculate energies for each frame and then print out an average at the end. If so, does it create a file with the calculated PG and GB energies per frame that I can then use to plot energy calculations for each frame? Is there any way I can examine the binding energy as a function of simulation time?
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, April 11, 2020 7:03 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests
On Fri, Apr 10, 2020, Cong Liu wrote:
>
>I recently compiled Amebr18 with GCC/8.3.0 and CUDA/10.1. The compilation
>went through well. However, *amber_cuda_serial *testing indicates 5 "*file
>comparison failure*": DPFP myoglobin_igb7, DPFP myoglobin_igb8, DPFP
>myoglobin_igb8_gbsa, DPFP irest1_ntt0_igb7_ntc2, DPFP irest1_ntt0_igb8_ntc2
>with "IEEE_UNDERFLOW_FLAG IEEE_DENORMAL" floating-point exceptions.
The underflow flag is not worrisome, but you should look at the .dif
files (collected in the logs folder) and see if the discrepancies look
like roundoff errors or something more serious.
....dac
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Received on Sat Apr 11 2020 - 08:00:01 PDT
