Re: [AMBER] Creating a water model from scratch

From: David Cerutti <>
Date: Mon, 8 Apr 2019 15:36:46 -0400

You need a good MD program and a shell script to modify the parameters to
files like ${AMBERHOME}/dat/leap/parm/frcmod.tip5p and
${AMBERHOME}/dat/leap/lib/solvents.lib. Then, apply whatever parameter
scanning strategy you wish. Use bigger water boxes to test the properties,
if they converge better with larger system sizes. You will not be able to
run a 2,000 atom system much faster than a 20,000 atom system, but if you
want to compromise and do 12,000 atom systems you can turn on the CUDA
Multi-process service and get an extra 80% throughput out of the newer GPUs
with 2-4 simulations running per card (as opposed to just one). With very
small systems you can get up to 140% additional throughput via MPS, but
again if more water in your simulation will help statistics as much as
longer timescales, then go with a bigger system size.

To start MPS:
set -e
export CUDA_MPS_PIPE_DIRECTORY=/tmp/nvidia-mps
export CUDA_MPS_LOG_DIRECTORY=/tmp/nvidia-log
nvidia-cuda-mps-control -d

To stop MPS:
echo quit | nvidia-cuda-mps-control


On Mon, Apr 8, 2019 at 2:56 PM Gustavo Seabra <>

> Hi all,
> I want to create a TIP5P water molecule from scratch. Does anyone know of
> a good resource I can use, like a step-by-step procedure, tutorial, etc?
> Thanks,
> Gustavo.
> Sent from Mail for Windows 10
> _______________________________________________
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Received on Mon Apr 08 2019 - 13:00:02 PDT
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