jslim-furame

YANK often fails in the minimization step since it employs GPUs. In such a case, MD softwares like Amber say that you have to use CPUs. So, you have to...

Thanks. As before, let us assume that there are 3 nodes and each node has 8-GPUs and thus total 24 GPUs available. In addition, let us imagine there are 48...

Thanks for your reply. You mean, even if I employ the GBSA (implicit water) model, i have to run the simulation during 20,000 (20 ns) or more. Right?

Yes. But I am using Boresch restraint. By the way, in this tutorial http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016, the author run the simulations during 1 ns/replica for complex system and 5 ns/replica for ligand...

[example.zip](https://github.com/choderalab/yank/files/3934734/example.zip) Please find attached my input files. As an input script for yank, I exactly used the t4-lysozyme implicit.yaml example except for employing Boresch restraint. To compare its result with...

Total number of electrons: 241; net charge: 0 INFO: Number of electrons is odd: 241 The error occurs because the number of electrons is odd. Please check the charge of...

Simply, bcc -nc 1 Its syntax follows antechamber. 2022년 9월 8일 (목) 21:02, kingljy0818 ***@***.***>님이 작성: > Thank you for your response. I have checked the charge of the ligand...