[gmx-users] Failure to preserve simulation temperature

[NG HUI WEN]

Hi all,

 

I have something here which I am would like to pick your brains. Thank
you in advance. In my trial-and-error attempt to equilibrate my membrane
protein system, I encountered this problem.

 

I was playing with 2 different mdp files (in succession), first by using
the Nose Hoover then v-rescale. I realised upon changing from the former
to the latter there was a drop in simulation temperature from 310K to
about 263K. Not sure if this have anything to do with the switch of
thermostat or due to some other parameter change?

 

 

The mdp file below which contain the Nose Hoover thermostat was used to
generate A3_1posre (see below grompp command)

title           = NPT

define          = -DPOSRES  

; Run parameters

integrator      = md            

nsteps          = 500000        ; 2 * 500000 = 1000 ps (1 ns)

dt              = 0.002         

; Output control

nstxout         = 50000         

nstvout         = 50000         

nstenergy       = 500           

nstlog          = 500           

; Bond parameters

continuation    = yes           

constraint_algorithm = lincs    

constraints     = all-bonds     

lincs_iter      = 1             

lincs_order     = 4             

; Neighborsearching

ns_type         = grid          

nstlist         = 5             

rlist           = 1.2           

rcoulomb        = 1.2           

rvdw            = 1.2           

; Electrostatics

coulombtype     = PME           

pme_order       = 4             

fourierspacing  = 0.16          

; Temperature coupling is on

tcoupl          = Nose-Hoover           

tc-grps         = Protein POPC SOL_CL-  

tau_t           = 0.1   0.1     0.1             

ref_t           = 310   310     310             

; Pressure coupling is on

pcoupl          = Parrinello-Rahman     

pcoupltype      = semiisotropic         

tau_p           = 5.0                   

ref_p           = 1.0   1.0             

compressibility = 4.5e-5        4.5e-5  

; Periodic boundary conditions

pbc             = xyz           

; Dispersion correction

DispCorr        = EnerPres      

; Velocity generation

gen_vel         = no            

; COM motion removal

nstcomm         = 1

comm-mode       = Linear

comm-grps       = Protein_POPC SOL_CL-

; Energy groups

energygrps      = Protein POPC SOL_CL-

 

I then use another mdp file containing v-rescale thermostat to extend
the simulation

 

grompp -f  v-rescale.mdp    -c  A3_1posre.gro  -o  A3_noposre.tpr   -n
index.ndx   -p topol_3.top

mdrun_mpi  -s  A3_noposre.tpr    -v   -cpi  A3_1posre.cpt

 

title           = NPT

define          =

; Run parameters

integrator      = md            

nsteps          = 1000000      ; 2 * 1000000 = 2000 ps (2 ns)

dt              = 0.002         ; 2 fs

; Output control

nstxout         = 250000                

nstvout         = 250000                

nstenergy       = 1000          

nstlog          = 500           

nstxtcout       = 250000                

; Bond parameters

continuation    = yes           

constraint_algorithm = lincs    

constraints     = all-bonds     

lincs_iter      = 1             

lincs_order     = 4             

; Neighborsearching

ns_type         = grid          

nstlist         = 10            

rlist           = 1.2           

rcoulomb        = 1.2           

rvdw            = 1.2           

; Electrostatics

coulombtype     = PME           

pme_order       = 4             

fourierspacing  = 0.12          

; Temperature coupling is on

tcoupl          = v-rescale             

fluctuation

tc-grps         = Protein POPC SOL_CL-  

tau_t           = 0.1   0.1     0.1             

ref_t           = 310   310     310             

; Pressure coupling is on

pcoupl          = Parrinello-Rahman     

pcoupltype      = semiisotropic         

tau_p           = 1.0                   

ref_p           = 1.0   1.0             

compressibility = 4.5e-5        4.5e-5  

; Periodic boundary conditions

pbc             = xyz           ; 3-D PBC

; Dispersion correction

DispCorr        = EnerPres      

; Velocity generation

gen_vel         = no            

; COM motion removal

; These options remove motion of the protein/bilayer relative to the
solvent/ions

nstcomm         = 1

comm-mode       = Linear

comm-grps       = Protein_POPC SOL_CL-

; Energy groups

energygrps      = Protein POPC SOL_CL-

 

 

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