Some useful tools related to Amber and DP.
Project description
dpamber
Some useful tools related to Amber and DP.
Installation
pip install dpamber
Tools
corr: generating data for DPRc models
corr
tool generates DeePMD-kit training data for DPRc from AMBER sander low-level QM/MM data and high-level data. For details of DPRc, read the DPRc paper.
Before using this tool, one need to prepare low-level and high-level QM/MM data:
$$ E_\text{hl}(\mathbf R)=E_\text{hl,QM}(\mathbf R)+E_\text{hl,QM/MM}(\mathbf R)+E_\text{MM}(\mathbf R) $$
$$ E_\text{ll}(\mathbf R)=E_\text{ll,QM}(\mathbf R)+E_\text{ll,QM/MM}(\mathbf R)+E_\text{MM}(\mathbf R) $$
Low-level and high-level data should use the same coordinate and the same MM method, but different QM methods. So, the correction energy for training will be
$$ \Delta E (\mathbf R) = E_\text{hl}(\mathbf R) - E_\text{ll}(\mathbf R) = (E_\text{hl,QM}(\mathbf R) - E_\text{ll,QM}(\mathbf R)) + (E_\text{hl,QM/MM}(\mathbf R) - E_\text{ll,QM/MM}(\mathbf R)) $$
An example of the command is
dpamber corr --cutoff 6. --qm_region ":1" --parm7_file some_param.param7 --nc some_coord.nc --hl high_level --ll low_level --out dataset
where --cutoff
takes cutoff radius of the QM/MM interaction for training. --qm_region
takes AMBER mask format for the QM region. --parm7_file
and --nc
take the PARM7 file and the trajectory (NetCDF) file, respectively. --ll
and --hl
are the prefixes of low-level and high-level files, including the mdout file (.mdout
), the mden file (.mden
) and the mdfrc file (.mdfrc
). The output dataset directory should be put in --out
.
See details from dpamber corr -h
.
devi: calculate model deviation
devi
can be used to calculate the model deviation of a given trajectory.
You need to install DeePMD-kit using
pip install dpamber[dpgpu]
See dpamber devi -h
for details.
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