Hello,
I would like to know the NCYC value that determines the number of steps for the steepest descent from the CHARMM-GUI-provided minimization scripts for AMBER MD simulation. Is it 2500 or 100 steps because the provided script is:
! Minimization options
imin=1, ! Turn on minimization
maxcyc=5000, ! Maximum number of minimization cycles
ncyc=2500, ! 100 steepest-descent steps, better for strained systems
Additionally, I would like to inquire about the applied restraint value in the CHARMM-GUI-provided minimization and equilibration scripts for AMBER MD simulation. Furthermore, I am interested in knowing the specific atoms for which the strain was applied. The obtained script:
! Restraint options
ntr=1, ! Positional restraints for proteins, sugars, and ligands
! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
/
&ewald
vdwmeth = 0,
/
Protein posres
1.0
RES 1 296 297 297
END
END
Finally, I would like to understand how the SHAKE constraint was applied even though the time step was 1 fs (dt=0.001) in the equilibration script provided by CHARMM-GUI for the AMBER MD simulation as follows:
! MD settings
nstlim=125000, ! 125K steps, 125 ps total
dt=0.001, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
Looking forward to hearing from you. Thanks!
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Received on Mon Aug 05 2024 - 12:30:02 PDT
