Haohao Fu comments

Results 37 comments of


                                            Haohao Fu

Diffrence between FEP and BAR in post-treatment of alchemical calculation

Generally BAR estimator yield smaller statistical error.

Problem with box size

Hi, groponp, I understand you problem. You can always set `WrapAll on` in your NAMD config file to circumvent this issue. I will think if it is possible to read...

FATAL ERROR: redistrib lone pair forces: no Lphost exists for LP 15891

This is because NAMD does not support lone pairs well. You can use the Amber force field to circumvent this issue.

FATAL ERROR: redistrib lone pair forces: no Lphost exists for LP 15891

CHARMM force filed introduces lone pairs for halozone bonds recently. However, this new feature has not been supported by the GPU version of NAMD.

Can a small DNA fragment be considered a ligand in BFEE

Yes. You can do it if the DNA is not too large

Can a small DNA fragment be considered a ligand in BFEE

I am not sure what "the PMF merge did not work" mean. You can load a set of consecutive `.czar.pmf` files and merge them into one file. Alternatively, you can...

Can a small DNA fragment be considered a ligand in BFEE

> Thank you for the reply and your suggestion, professor. I'm sorry, but I still have one question for you. When I add the consecutive .czar.pmf files and try to...