[AMBER] Electrostatic energy in TI at lambda=1 for a toy system

From: Ali Morshedi <morshedi1370.gmail.com>
Date: Sat, 11 Dec 2021 02:04:27 -0600

Dear all,

I have two toy systems: system 1 is a single water molecule: O_wat(-0.5),
H1_wat(0.25), H2_wat(0.25) and system 2 is NaOH: Na+(+1), O_oh(-1.25),
H1_oh(0.25) --charges in parantheses--. I use parmed's tiMerge to combine
them and get a system with 6 atoms(and 3 residues: Na+, WAT and OH). In TI,
timask1=:WAT, timask2=:Na+,OH and scmask1=:WAT.H2, scmask2=:Na+. I expect
the initial electrostatic energy at lambda=0.0 to be equal to the EELEC of
system 1 and similarly at lambda=1.0 to system 2. However the values I'm
getting do not match at lambda=1.0. Please find attached all the files
needed. I'd appreciate it if you could let me know what I'm missing.

Here are some more details on attached files:
wat.parm7, wat.rst7: single water molecule. gives EELEC = 0.0
oh.parm7, oh.rst7: single NaOH. gives EELEC = -114.4056
ti.parm7, ti.rst7: gives EELEC(lambda=0) = 0.0, EELEC(lambda=1.0)
= -88.4867
run.sh: runs the above

Thanks in advance,
Ali


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Received on Sat Dec 11 2021 - 00:30:02 PST