[gmx-users] wierd behavior of mdrun

[Mark Abraham]

Paymon Pirzadeh wrote:
> 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!

Check that a short version of this job runs fine on a local machine. 
Probably you are having some problem with a file system and/or its 
buffering. Inspect your quotas. Talk to your system admins.

Mark

> 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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> 
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