[gmx-users] Failure to preserve simulation temperature

[Justin A. Lemkul]

NG HUI WEN wrote:
> 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
> 
>  

The problem is likely here.  You're switching the conditions of the ensemble 
during mdrun.  Normally, you would supply the .cpt file to grompp -t to preserve 
all the state variables.  In conjunction with "gen_vel = no" in the .mdp file, 
the continuation is exact.  Since you're not generating velocities with grompp 
AND not supplying a .cpt file, the initial state will be hard to predict, but 
likely will not correspond to the proper ensemble.

-Justin

> 
> 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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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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