| 3:13:35 PM PST - Wed, Dec 4th 2013 |
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Please ignore this message. It seems this approach (using 'center' in rewriting restart files) might cause a huge error in free energy calculation because the QM region of each bead will not be the same (their positions are shifted). Sorry for any confusion.
Quote:Tpirojsi Dec 4th 7:34 pmHi Jingbo,
Glad for having someone to discuss the issue with. For some reason, your approach doesn't help in my case but it's good to know and I'll keep that in mind too. This error seems to be a common error that I think coming from many reasons. Other than what I explained above, when doing FEP calculation I also still have seen this error arising even though the waters were in the perfect shape and place, i.e. no clumping waters or bad contacts. My solution was rewriting restart files from NEB beads with the 'center' keyword in prepare module and using the new restart files to run FEP calculations. Also make sure that we use these new restart files in gerenating xyzi and esp files too.
UPDATE Although the approach sometimes fixes my problem in case this error arises in FEP calculation, it still doesn't seem to completely get rid of the problem.
Best,
Tee
Quote:Wjb0920 Nov 27th 2:41 amDear Tpirojsi,
Here I provide another way to solve the problem. The increase of cutoff from 0.9nm to 1.2nm in MD directives group, and also change bqzone from 9 to 12 in qmmm directive group may go through the simulation without error of deviation too large.
Best,
Jingbo |
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