Hi,
I have been using Amber 20 for the production in NPT CPHMD explicit
solvent. Now, using the same input files with Amber22 I get the error that
currently constant pressure CPHMD is not possible. How can I solve this?
Thanks in advance,
Mahdi
-------------------------------------------------------
Amber 22 PMEMD 2022
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 22
| Compiled date/time: Thu Apr 14 20:06:37 2022
| Run on 08/03/2023 at 12:04:33
| Executable path: /opt/science/amber/amber22/bin/pmemd.cuda
| Working directory: /home/mkalhori/replica_hASIC1a_des
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: step7_production.mdin
| MDOUT: step7_rep1.mdout
| INPCRD: step6.6_equilibration.rst7
| PARM: inp-cph-d.parm7
| RESTRT: step7_rep1.rst7
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: step7_rep1.nc
| MDINFO: step7_rep1.mdinfo
| MDFRC: mdfrc
Here is the input file:
A NPT simulation for common production-level simulations
&cntrl
imin=0, ! No minimization
irest=1, ! This IS a restart of an old MD simulation
ntx=5, ! So our inpcrd file has velocities
ig=-1,
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
temp0=310, ! Target temperature
! Potential energy control
cut=12.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=100000000, ! 1 ns (500K) total--200ns
dt=0.002, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=1000, ! Print energies every 1000 steps
ntwx=50000, ! Print coordinates every 50000 steps to the trajectory
ntwr=10000, ! Print a restart file every 10K steps (can be less
frequent
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
! Constant pressure control.
barostat=1, ! Berendsen barostat... change to 2 for MC
ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/
surften
pres0=1.0, ! Target external pressure, in bar
taup=1.0,
! Constant surface tension (needed for semi-isotropic scaling).
Uncomment
! for this feature. csurften must be nonzero if ntp=3 above
csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso
scaling
ninterface=2, ! Number of interfaces (2 for bilayer)
! constant pH flags
icnstph=2, ! should be set to 2 to toggle explicit solvent cphmd
ntcnstph=500, ! is the number of steps between attempted protonation
stat
solvph=5.0, ! is the solution pH
ntrelax=100, ! is the number of steps of relaxation dynamics you wish
to
saltcon=0.1, ! is the GB salt concentration (and only used in the
proto
! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
/
Note: ig = -1. Setting random seed to 132730 based on wallclock time in
microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
*| ERROR: Currently, constant pH simulations cannot be executed at
constant pressure! Input errors occurred. Terminating execution.*
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Received on Thu Aug 03 2023 - 04:00:02 PDT
