[gmx-users] REMD slow's down drastically

[Francis Jing]

Because every replica has to be calculated separately, it seems the speed
is not that slow (125 * 0.07 ~ 9 ns).

Also, to evaluate it, you should post how many CPUs you used, and other
information like exchange attempt frequency...


Francis


On Mon, Feb 24, 2014 at 3:32 PM, Singam Karthick <sikart21 at yahoo.in> wrote:

> Dear members,
> I am trying to run REMD simulation for poly Alanine (12 residue) system. I
> used remd generator to get the range of temperature with the exchange
> probability of 0.3. I was getting the 125 replicas. I tried to simulate 125
> replicas its drastically slow down the simulation time (for 70 pico seconds
> it took around 17 hours ) could anyone please tell me how to solve this
> issue.
>
> Following is the MDP file
>
> title           = G4Ga3a4a5 production.
> ;define         = ;-DPOSRES     ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 12500000      ; 2 * 5000000 = 3ns
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 0             ; save coordinates every 0.2 ps
> nstvout         = 10000         ; save velocities every 0.2 ps
> nstxtcout       = 500           ; save xtc coordinate every 0.2 ps
> nstenergy       = 500           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = yes           ; Restarting after NVT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = hbonds        ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> morse           = no
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cels
> nstlist         = 5             ; 10 fs
> rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         =  protein SOL Cl       ;two coupling groups - more
> accurate
> tau_t                 = 0.1 0.1  0.1 ; time constant, in ps
> ref_t                 = XXXXX  XXXXX  XXXXX    ; reference temperature,
> one for each group, in K
> ; Pressure coupling is on
> pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
> pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 2.0           ; time constant, in ps
> ref_p           = 1.0           ; reference pressure, in bar
> compressibility = 4.5e-5        ; isothermal compressibility of water,
> bar^-1
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
>
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
>
>
> regards
> singam
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-- 
Zhifeng (Francis) Jing
Graduate Student in Physical Chemistry
School of Chemistry and Chemical Engineering
Shanghai Jiao Tong University
http://sun.sjtu.edu.cn