GROMACS version:5.1.4
GROMACS modification: No
I am trying to shear a 5x5x5 box of SPCE water by using the deform mdp option. The gromacs documentation is vague about the anisotropic pressure coupling option as well as compressibility option. This is my mdp file :
;simple shear simulation of 5x5x5 nm^3 water box with SPC/E model with deform
;Written by Sriram Krishnamurthy on 17/11/2020
;################ Run Control ###################
integrator = md ; leap-frog algorithm
dt = 0.002 ; 2fs
nsteps = 2500000 ; 2fs x 2500000 steps = 5000 ps = 5 ns
;##############Output Control ###################
nstxout = 1000 ; no. steps elapse before writing coordinates to .trr
nstvout = 1000 ; no. steps elapse before writing velocities to .trr
nstfout = 1000 ; no. steps elapse before writing forces to .trr
nstlog = 1000 ; no. steps elapse before writing energies to log files
nstcalcenergy = 500 ; no. steps elapse before calculating energies
nstenergy = 500 ; no. steps elapse before writing energies to energy file
compressed-x-precision = 500 ; compressed trajectory file
;############### Neighbour Searching #############
cutoff-scheme = Verlet
nstlist = 40 ; frequence to update neighbour list
pbc = xyz
;verlet-buffer-tolerance = 0.01 ; [KJ/(mol ps)]
;rlist = 1.2 ; nm
comm-mode = Linear
nstcomm = 200
;############### Electrostatics ################
coulombtype = PME
rcoulomb = 1.2 ; cut-off distance for Coulomb (nm)
;###############Van der Waals ##################
vdwtype = Cut-off
rvdw = 1.2 ; L-J cut-off distance (nm)
;############### Ewald ##################
pme-order = 4
fourierspacing = 0.08
;############### Temperature Coupling ############
tcoupl = berendsen
tc-grps = Water
tau-t = 0.1 ; time constant for thermostat (ps)
ref-t = 310 ; reference temperature of reservoir (K)
nsttcouple = 10
**;###############Pressure Coupling ################**
**pcoupl = Parrinello-Rahman ;**
**pcoupltype = anisotropic**
**nstpcouple = 10**
**tau-p = 0.4**
**compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0; compressibility of water @300K**
**ref-p = 1.0 1.0 1.0 0 1.0 1.0**
;################Velocity generation ###############
gen-vel = no;
;################### Constraints #################
constraints = h-bonds
constraint-algorithm = LINCS
lincs-order = 4
continuation = yes ; continuing after npt run
From what I understand,
- I cannot use all off-diagonal pressures as no-zero
- Off diagonal compressibilities should not be zero for a deform simulation.
- All ref-p cannot be equal to 1.0, I don’t know which to put equal to 0.
What options should I used for ref-p and compressibilities to perform a simple shear simulation?