[gmx-users] Final Temp = 303 K ?

[XAvier Periole]

On Jun 18, 2009, at 11:57 PM, 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 unfortunately the 303 K is what you should expect. This is
small deviation that results from some approximation made. This
is the best you can get. It is fine.

If you want you can play a bit with the cutoff options you have and
see the effect. For exemple you have a 9-1.4 nm twing-range
cutoff and you update every 5 steps. Reducing the update to 1
would certainly reduce the 303 closer to 300 K. And also reducing
1.4 to 1.2 nm should have the same effect. This is due to the
  fact that you update the forces for atoms within 9-1.4 only every 5
steps.

check the literature and google on cutoff effect ... you'll find a lot
on it.
>
>
>
> 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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