[AMBER] tleap/xleap performance enhancement

From: Himanshu Joshi <himanshuphy87.gmail.com>
Date: Thu, 6 Feb 2020 16:48:58 -0600

Dear AMBERites,


I am using tleap to load a pre- equilibrated large pdb file containing ~10
million water molecules to create new input files.

Although, I could manage to tweak the pdb file format to get recognized by
tleap but the process of generating the topology and coordinate file is
slower, (approximately 12 hours for 1 million atoms).

Can anyone please suggest some ways to enhance the performance xleap/tleap
process. The most time consuming process is when it prints "Starting new
chain with *segname*" . Will it help if we somehow disable the print

I am running tleap on a machine having 2 intel xeon cores, given that leap
does not a support gpu/parallel processing (if I understand it correctly),
is there a way to improve the timing for creating the amber topology and
coordinate files.

Looking forward to your recommendations.

Thank you for you valuable time and consideration.

*With Regards,HIMANSHU JOSHI *
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Received on Thu Feb 06 2020 - 15:00:02 PST
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