Dear Amber users,
I always perform minimisation using the ntb=1 and therefore with periodic boundary under constant volume.
I am attempting to simulate membrane protein now. I have generated membrane using CHARMM GUI and this is the minimisation control file that was generated for me by the software:
Minimization input file in explicit solvent
&cntrl
! Minimization options
imin=1, ! Turn on minimization
maxcyc=5000, ! Maximum number of minimization cycles
ncyc=2500, ! 100 steepest-descent steps, better for strained systems
! Potential energy function options
cut=12.0, ! Nonbonded cutoff, in Angstroms
fswitch=10.0, ! Force-based switching
! Control how often information is printed to the output file
ntpr=100, ! Print energies every 100 steps
ntxo=2, ! Write NetCDF format
! Restraint options
ntr=1, ! Positional restraints for proteins, sugars, ligands, and lipid head groups
nmropt=1, ! Dihedral restraints for sugars and lipids
! 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,
/
&wt
type='END'
/
Protein posres
10.0
RES 1 227
END
Membrane posres
2.5
FIND
P * * POPC
SEARCH
RES 1 11740
END
END
DISANG=step6.0_minimization.rest
LISTIN=POUT
LISTOUT=POUT
The ntb is not set to 1. Can I proceed with this?
Thank you
L.
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Received on Wed Nov 28 2018 - 10:00:02 PST
