[gmx-users] volume not shrinking when restrains present

[p buscemi]

My apologies for sparce information.
Gromacs 2019, run on either dual rts 2080 ti or gtx 1080ti
A sample npt.mdp that fails to collapse:

;title = OPLS NPT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; md = leap-frog integrator
nsteps = 500000 ; 2 * 50000 = 100 ps
dt = 0.0012; 2 fs

; Output contro
nstxout = 5000 ; save coordinates every 1.0 ps
nstvout = 5000 ; save velocities every 1.0 ps
nstenergy = 5000 ; save energies every 1.0 ps
nstlog = 5000 ; update log file every 1.0 ps

; Bond parameters
continuation = yes ; Restarting after NVT **********************
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS normally 1
lincs_order = 4 ; also related to accuracy normally4

; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid
nstlist = 40
rcoulomb = 1.0
rvdw = 1.0 )
vdw-type = cut-off
verlet-buffer-tolerance = 1.4e-4 ; *****************************

; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT

; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Z8G5
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K

; Pressure coupling is on
pcoupl = Berendsen ; Parrinello-Rahman
pcoupltype = surface-tension
tau_p = 2.0
ref_p = 1.0 1.0
compressibility = 4.5e-5 5.5e-5
refcoord_scaling = com

; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
;DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; no = Velocity generation is off *******************************
gen-temp = 200

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On Jun 5 2019, at 12:48 pm, p buscemi <pbuscemi at q.com> wrote:
>
> Dear Users,
> I've been trying to solve this for several days. A box with 100 polymer strands restrained in only the x direction on either end is built and under nvt the strands will coalesce into groups of 8-15 molecules. Under npt isotropic or semiisotropic or surface-tension, the box will not collapse in the y or z direction. If the restraints are removed the box will shrink and the elongated polymers "ball-up" as expected. Should restraints affect the decrease in box volume in this manner ?
> Thanks for any comments...
> Paul
>
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