Hello,
I have a question regarding the tishake flag used for AFE simulations using pmemd.cuda. As I understand, the noshakemask should be applied to the part of the system that is changing - I am applying this to the same atoms as in timask1 and timask2.
In the manual, it states that for the default tishake=0:
"coordinates are synchronised after SHAKE, no constraints removed".
For tishake=2, it states that:
"SHAKE is kept in bonds containing one common and softcore atom(s). This experimental option maintains the physical bond length as specified by the forcefield across all lambda windows in a relative binding free energy calculation."
If tishake=2 specifies that SHAKE is kept in bonds between common and softcore atoms, does this mean that the SHAKE is applied to the atoms that are in the noshakemask?
As for tishake=0, as it states no constraints removed, does this mean SHAKE is applied still to the atoms in the noshakemask? Is this then not effectively the same thing as tishake=0? Or does tishake=0 not have SHAKE applied between common and softcore atoms by default?
I apologise in advance if the explanation is obvious, but I think I'm struggling to understand the specifics of how SHAKE is applied during TI in each case based on the manual.
Best wishes,
Anna
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Received on Tue Dec 17 2024 - 10:00:03 PST
