[gmx-users] REMD slow's down drastically

[Francis Jing]

So what's the difference between the two systems? I think you can look
through the end of the log file, and find which part slowed down. Maybe
your job did not use the right partition of cores (too much comm. time)? I
don't know.

Francis
On 25 Feb, 2014 1:19 am, "Singam Karthick" <sikart21 at yahoo.in> wrote:

> Dear Francis
> we are running in the  Xeon E5-2670 8C 2.60GHz (2 CPUs , 8 cores, 16
> threads) for each temperature. and the exchange attempt frequency is 500
> steps. The other system with 126 replicas run 30 ns per day ( system size
> of  ~38000 atoms). could you please help us in solving this problem
>
> regards
> singam
>
>
>
> On Monday, 24 February 2014 1:02 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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