[gmx-users] wierd behavior of mdrun

[Paymon Pirzadeh]

I made a .tpr file for my md run without any problems (using the bottom
mdp file). My job submission script is also the same thing I used for
other jobs which had no problems. But now when I submit this .tpr file,
only an empty log file is generated! The qstat of the cluster shows that
the job is running, also the processors are 100% engaged while I have no
outputs!
Here is my mdp file:
 title            = Yo
cpp              = cpp
include          = -I../top
define           = -DPOSRES

; Run control

integrator       = md
dt               = 0.001           ;1 fs
nsteps           = 3000000         ;3 ns
comm_mode        = linear
nstcomm          = 1

;Output control

nstxout          = 5000
nstlog           = 5000
nstenergy        = 5000
nstxtcout        = 1500
nstvout          = 5000
nstfout          = 5000
xtc_grps         =
energygrps       =

; Neighbour Searching

nstlist          = 10
ns_type          = grid
rlist            = 0.9
pbc              = xyz

; Electrostatistics

coulombtype      = PME
rcoulomb         = 0.9
;epsilon_r        = 1

; Vdw

vdwtype          = cut-off
rvdw             = 1.2
DispCorr         = EnerPres

;Ewald

fourierspacing  = 0.12
pme_order       = 4
ewald_rtol      = 1e-6
optimize_fft    = yes

; Temperature coupling

tcoupl           = v-rescale
ld_seed          = -1
tc-grps          = System
tau_t            = 0.1
ref_t            = 275

; Pressure Coupling

Pcoupl           = no
;Pcoupltype       = isotropic
;tau_p            = 1.0
;compressibility  = 5.5e-5
;ref_p            = 1.0
gen_vel          = yes
gen_temp         = 275
gen_seed         = 173529
constraint-algorithm     = Lincs
constraints      = all-bonds
lincs-order              = 4

I am not sure where things go wrong!

Payman












On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
> Paymon Pirzadeh wrote:
> > Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> > negative charge exactly? Does that hurt science or simulation?
> 
> It's probably irrelevant. The representation of "decimal" numbers on 
> computers can be inexact, such that things like 0.02 added to itself 100 
> times does not pass a test for equality with 2. You may be observing 
> this kind of thing here. Your protein's [atoms] directive has a running 
> count of the total  charge on the molecule - go and read it and see that 
> each residue has an integral charge. Hopefully you can observe where the 
> rounding error might be occurring and you can make a judgement about 
> whether this might be true.
> 
> Mark
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