Hi Andrea,
The TI limit of 200 atoms was set based on the assumption that TI regions should only contain few atoms. The design of the whole TI-GPU part is based on this assumption.
Scientifically, TI/FEP are only practically useful when the perturbation is small. I would not suggest to do something like 200-atom mutated to nothing. Even you could do this kind of simulations, I don't think you will get any meaningful results--likely the errors will be huge.
If this is a community consensus, technically we could increase the limit but it would also impact the performance because some pre-defined arrays on GPU would require more memory,...etc.
Taisung
-----Original Message-----
From: Andrea Cavalli <andrea.cavalli.irb.usi.ch>
Sent: Wednesday, March 27, 2019 4:15 AM
To: amber.ambermd.org
Subject: [AMBER] TI atom limit
Hello,
I want to use TI to decouple a protein in a dimer and compute the absolute free energy of binding. Unfortunately there is a limit of 200 atoms.
Is there a way to increase it? (By changing the code) Andrea
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Andrea Cavalli
Group Leader. Computational Structural Biology Institute for Research in Biomedicine Università della Svizzera Italiana Via Vincenzo Vela 6
CH-6500 Bellinzona
Phone : +41 91 820 0391
Fax: : +41 91 820 0305
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Received on Wed Mar 27 2019 - 05:00:03 PDT
