Are the ionizable residues part of the “pulling group” or “reference group” definitions? If so, is there a way to try some other definitions for the groups that do not include residues that may change in the course of the simulation?
Gustavo Seabra
> Em 7 de dez de 2015, à(s) 11:25, zhonghe xu <zhonghexu01.163.com> escreveu:
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> Hi Amber Users：
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>
> I used Amber14 to run SMD (jar) simulations combined with explicit solvent constant pH.
> I also analysed the distance between pulling group and reference group using distance
> command in cpptraj module. Then I found the results (distance vs time) obtained from analysis of
> trajectory are severely deviated from standard output of jar, which can be seen in below figure.
> By the way, I also excluded periodic boundary condition (image) effect during analysis the distance,
> and the aforementioned problem was never found in previous SMD (jar) simulations without constant pH
> for same system.
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> Thanks in advance!
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> Zhonghe Xu
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Received on Mon Dec 07 2015 - 12:00:03 PST
