[gmx-users] Final Temp = 303 K ?

[Chih-Ying Lin]

Hi
Here is my whole md.mdp.
 But the final Temp = 303 K
 No matter I extend the simulation time, the final Temp = 303 K and it
 can not reach the ref_t = 300 K

 Does it make sense?



 The simulation system is protein + ligand + counter ions.
 ligand is the 33-atom molecule.
 force field ffG45a3.


 Thank you
 Lin




; VARIOUS PREPROCESSING OPTIONS
title                    = Lysozyme
cpp                      = /lib/cpp

; RUN CONTROL PARAMETERS
integrator               = md
tinit                    = 0       ; Starting time
dt                       = 0.002   ; 2 femtosecond time step for
integration
nsteps                   = 250000 ; 500 picoseconds total simulation time
comm_mode                = Linear  ; Removing overall translations from
the system
nstcomm                  = 1       ; ... and doing so every step

; OUTPUT CONTROL OPTIONS
nstxout                  = 1000 ; Writing full precision coordinates
every nanosecond
nstvout                  = 0     ; Writing velocities every nanosecond
nstfout                  = 0     ; Not writing forces
nstlog                   = 0     ; Writing to the log file every step
nstenergy                = 1000   ; Writing out energy information every step
nstxtcout                = 1000   ; Writing coordinates every step
xtc_precision            = 1000  ; Floating point number to integer
scaling
xtc-grps                 = System
energygrps               = Protein Non-Protein

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = Reaction-Field
rcoulomb                 = 1.4
epsilon_rf               = 78
epsilon_r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.4

; Temperature coupling
Tcoupl                   = Berendsen
tc-grps                  = Protein  Non-Protein
tau_t                    = 0.1      0.1
ref_t                    = 300      300
; Pressure coupling
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
gen_temp                 = 300.0
gen_seed                 = 173529

; OPTIONS FOR BONDS
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = yes
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30