[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

[Berk Hess]

Hi,

In this manner you use the same random seed and thus noise for all parts.
In most cases this will not lead to serious artifacts with SD,
but you can never be sure.
When checkpoints are used, you do not repeat random numbers.
This also gives a difference between serial and parallel in 4.0.
With serial you get exactly the same noise per atom, in parallel not,
since atoms migrate from one node to another (with domain decompostion).

If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv.

Berk


> Date: Wed, 4 Feb 2009 15:05:47 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] micelle disaggregated in serial, but not parallel,	runs using sd integrator
> 
> Thank you Berk,
> 
> I will loon into tau_t=1.0 (or at least not = 0.1). Thank you for the hint.
> 
> These simulations run in 200 ps segments and utilize restarts via  
> grompp -t -e like this:
> 
> EXECUTING:  
> /hpf/projects1/pomes/cneale/exe/gromacs-4.0.3/exec/bin/grompp -f  
> /scratch/4772976.1.ompi-4-21.q/md6_running/dpc50_md6.mdp  -c  
> md5_success/dpc50_md5.gro -p dpc50.top -n dpc50.ndx -o  
> /scratch/4772976.1.ompi-4-21.q/md6_running/dpc50_md6.tpr -maxwarn 1 -t  
> md5_success/dpc50_md5.trr -e md5_success/dpc50_md5.edr
> 
> The -maxwarn 1 is to avoid this message:
> 
> WARNING 1 [file  
> /scratch/4772976.1.ompi-4-21.q/md5_running/dpc50_md5.mdp, line unknown]:
>    Can not couple a molecule with free_energy = no
> 
> which I don't think should be a problem.
> 
> ###
> 
> I didn't check temperatures previously, but I did check the energy  
> components output the the .log file in zero step mdruns in both serial  
> and parallel and found no difference.
> 
> Here is the information on temperature and total energy for the serial  
> and parallel runs:
> 
> For the run in parallel:
> 
> Last energy frame read 780 time 7800.000
> 
> Statistics over 1950001 steps [ 0.0000 thru 7800.0000 ps ], 1 data sets
> All averages are exact over 1950001 steps
> 
> Energy                      Average       RMSD     Fluct.      Drift   
> Tot-Drift
> -------------------------------------------------------------------------------
> Temperature                 303.322    901.905    901.905 -6.34952e-06  
> -0.0495263
> Heat Capacity Cv:     -1.01712 J/mol K (factor = 8.84124)
> 


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