Date: Fri, 4 Oct 2024 16:42:42 +0000
Hello,
What reaction or movement are you interested in? If it involves hydrogen bond movement in the QM region, set qmshake=0 in the &qmmm portion. You can leave ntc=2/ntf=2 in the &cntrl area. This removes shake from the QM region but maintains it for the MM.
Sincerely,
Peter Ramdhan, PharmD
2nd Year PhD Student
Dept. of Medicinal Chemistry, Li Lab
University of Florida College of Pharmacy
[cid:0a5acbff-8ceb-4647-ad3b-837584b9fb21]
________________________________
From: Dutta, Ankita via AMBER <amber.ambermd.org>
Sent: Friday, October 4, 2024 12:13 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] QM/MM simulation with SHAKE using Sander QUICK module
[External Email]
Hello,
I am relatively new to using AMBER, specifically the QUICK module.
I am trying to study the reaction mechanism between a ligand and the residues in the active site of a protein of interest.
The QUICK input file I am using is as follows:
&cntrl
imin=0, nstlim=1000000, ! 2ns QM/MM simulation
dt=0.002, irest=1, ntx=7, ! 2 fs time step 1ns sim
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
ntf=2, ntc=2, ! Shake hydrogen atoms
ntpr = 1000, ntwx = 1000, ntwr = 1000
cut=8.0, ! 8 angstrom classical non-bond cut off
ifqnt=1 ! Switch on QM/MM coupled potential
/
&qmmm
qmmask='.4460, 4461, 4499, 4500, 7544, 7553', !
qm_theory='quick', ! Use the PM3 semi-empirical Hamiltonian
qmcut=8.0 ! Use 8 angstrom cut off for QM region
/
&quick
method = 'B3LYP',
basis = 'def2-svp',
/
My question is: How does SHAKE work in QM/MM simulation. Are the bonds between the atoms in the 'qmmask' included in the SHAKE protocol?
I have so far obtained a 100ps long QM/MM trajectory from the above simulation. Upon visualizing the trajectory, I see that the bond lengths between the atoms specified in the qmmask do not change over time. So I am bit confused as bond length fluctuations would be necessary for a reaction to occur.
Would really appreciate it if someone could recommend the appropriate SHAKE specification for QUICK simulations. Also any advice on the input file above is welcomed!
Best,
Ankita Dutta, PhD
Postdoctoral Fellow
Icahn School of Medicine at the Mount Sinai Hospital
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