[gmx-users] NVT error

Mehreen Jan mehreen_jan1990 at yahoo.com
Fri Feb 10 12:40:21 CET 2017


VNT error:
5.0.7
ff 43A1
error:
Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values


 read from gromacs mail list "Precisely what it says. You specify one group to be coupled (System), but then
provide coupling information for two groups." i have no idea to correct my own NVT and NPT

title		= OPLS Lysozyme NVT equilibration 
define		= -DPOSRES	; position restrain the protein
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 50000		; 2 * 50000 = 100 ps
dt		= 0.002	        ;	 
; Output control
nstxout		= 5000		; save coordinates every 0.2 ps
nstvout		= 5000		; save velocities every 0.2 ps
nstenergy	= 5000		; save energies every 0.2 ps
nstlog		= 1000		; update log file every 0.2 ps
; Bond parameters
continuation	= no		; first dynamics run
constraint_algorithm = lincs	; holonomic constraints 
constraints	= H-bonds	; all bonds (even heavy atom-H bonds) constrained
lincs_iter	= 1		; accuracy of LINCS
lincs_order	= 4		; also related to accuracy
; Neighborsearching
ns_type		= grid		; search neighboring grid cells
nstlist		= 5		; 10 fs
rlist		= 1.0		; short-range neighborlist cutoff (in nm)
rcoulomb	= 1.0		; short-range electrostatic cutoff (in nm)
rvdw		= 1.0		; short-range van der Waals cutoff (in nm)
; 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		= HEM   	; two coupling groups - more accurate
tau_t		= 0.1	0.1	; time constant, in ps
ref_t		= 300 	300	; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl		= no 		; no pressure coupling in NVT
; Periodic boundary conditions
pbc		= xyz		; 3-D PBC
; Dispersion correction
DispCorr	= EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel		= yes		; assign velocities from Maxwell distribution
gen_temp	= 300		; temperature for Maxwell distribution
gen_seed	= -1		; generate a random seed


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