[gmx-users] Final Temp = 303 K ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 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?
> 
> 

Yes, and I explained why.  Specify options yourself, don't rely on defaults!

-Justin

> 
>  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
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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