[gmx-users] Re: job failed

[Mark Abraham]

On 6/04/2012 3:36 PM, Albert wrote:
> hello:
>
>   thank you very much for your kind messages. I first did 
> minimization, the NVP with gradually heating the system from 0-310K, 
> and them NPT production:
>
> ----NVT.mpd---------------
> define         = -DPOSRES  -DPOSRES_LIG
> constraints    = hbonds
> integrator    = md
> dt        = 0.001 ; ps !
> nsteps        = 3000000 ; total 3000.0 ps.
> nstcomm        = 10
> nstxout        = 5000 ; collect data every 1.0 ps
> nstxtcout    = 5000
> nstvout        = 5000
> nstfout        = 0
> nstlog        = 10
> nstenergy    = 50
> nstlist        = 10
> ns_type        = grid
> rlist        = 1.2
> coulombtype    = PME
> rcoulomb    = 1.2
> vdwtype        = cut-off
> rvdw        = 1.4
> pme_order    = 4
> ewald_rtol    = 1e-5
> optimize_fft    = yes
> DispCorr    = no
> ; Berendsen temperature coupling is on
> Tcoupl        = v-rescale
> tau_t        = 0.1    0.1
> tc-grps        = protein non-protein
> ref_t        = 310    310
> ; Pressure coupling is off
> Pcoupl        = no
> Pcoupltype    = isotropic
> tau_p        = 1.0
> compressibility    = 4.5e-5
> ref_p        = 1.0
> pbc             = xyz
> annealing         = single    single
> annealing_npoints     = 2        2
> annealing_time         = 0 5000    0 5000
> annealing_temp         = 0 310    0 310
> gen_vel                  = no
> constraint_algorithm     = Lincs
>
>
> ---NPT md.mdp--------------------------
> constraints    = hbonds
> integrator    = md
> dt        = 0.002 ; ps !

This time step is normally too long for those constraints. See manual 6.5.

> nsteps        = 5000000 ; total 10ns.
> nstcomm        = 10
> nstxout        = 20000 ; collect data every
> nstenergy       = 20000
> nstxtcout       = 20000
> nstvout        = 0
> nstfout        = 0
> nstlist        = 10
> ns_type        = grid
> rlist        = 1.2
> coulombtype    = PME
> rcoulomb    = 1.2
> vdwtype        = cut-off
> rvdw        = 1.4
> pme_order    = 4
> ewald_rtol    = 1e-5
> optimize_fft    = yes
> DispCorr    = no
> ; Berendsen temperature coupling is on
> Tcoupl        = v-rescale
> tau_t        = 0.1    0.1
> tc-grps        = protein    non-protein
> ref_t        = 310    310
> ; Pressure coupling is on
> Pcoupl        = parrinello-rahman

Don't use algorithms that are known to be unstable for equilibration 
while you are doing equilibration. See manual.

> Pcoupltype    = isotropic
> tau_p        = 1.0
> compressibility    = 4.5e-5
> ref_p        = 1.0
> ; Generate velocites is on at 310 K.
> gen_vel        = yes

Why bother doing slow heating if you're just going to re-initialize with 
random velocities again?

Mark

> gen_temp    = 310.0
> gen_seed    = 6666
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120406/8fc4d2fb/attachment.html>