[gmx-users] the calculation time

[Mark Abraham]

On 01/10/11, ahmet yıldırım  <ahmedo047 at gmail.com> wrote:
> Dear Justin and Mark,
> 
> I want to investigate the structure xxx.pdb. When I run "the run.mdp" the gromac shows that will end in 25 days. What kind of changes do you recommend in "the run.mdp file" to reduce/short the calculation time? Or, Is there any error/missing in the file? My run.mdp inputsc-ript is the following.
> 
> 
> PC hardware:İntel Core I7 (four core), 6GB RAM
> 
> Thanks in advance
> 
> "The run.mdp"
> title           = MD
> cpp             = /usr/bin/cpp
> constraints     = all-bonds
> integrator      = md
> 
> dt              = 0.002    ; ps !
> nsteps          = 10000000 ; total 20000 ps = 20 ns.
> nstcomm         = 1
> nstxout         = 100000    ; collect data every 200 ps
> nstvout         = 100000
> nstfout         = 0
> 
> nstlog          = 1000
> nstenergy       = 1000
> nstlist         = 10
> ns_type         = grid
> rlist           = 1.0
> coulombtype     = PME
> rcoulomb        = 1.0
> vdw-type    = cut-off
> rvdw            = 1.4
> 

That's an excessively large value for rvdw. You should be trying to aim at .mdp parameter values that match those with which the force field was parameterized (or has since been shown to work well with).


> 
> 
> fourierspacing  = 0.12
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl          = berendsen
> tc-grps         = Protein non-protein
> 
> tau_t           = 0.1 0.1 
> ref_t           = 300 300 
> ; Energy monitoring
> energygrps      = Protein non-protein
> ; Pressure coupling 
> Pcoupl          = berendsen
> tau_p           = 1.0
> compressibility = 5e-5 5e-5 5e-5 0 0 0
> 
> ref_p           = 1.0
> 
> 

It's a fact of life that atomistic MD with explicit solvent is a computationally expensive business. If 25 days is too many, you need to consider using a smaller system, getting (access to) better hardware, using a coarse-grained model, or using implicit solvation.

Mark
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