[gmx-developers] Double precision restarts are exact, single precision are not in gromacs 3.2.1

[Mark Abraham]

Hi,

After posting twice to gmx-users about this problem and apparently being 
ignored, I've done yet more testing and discovered a clear difference in 
the way single precision and double precision gromacs handle MD restarts 
in version 3.2.1 (using Berendsen thermostat and barostat, and PME, on 
Pentium 4 architecture).

Single precision restarts using the previous run's trajectory (.trr) and 
energy (.edr) files to obtain the configuration and other information 
(and using unconstrained_start = yes, and gen_vel = no in the .mdp file 
to make sure that the old configuration is preserved) do in fact 
reproduce the configuration exactly, in that the energy components 
calculated by the force field are identical in Step 0 of the restart 
with those of the final Step in the previous run. However the total 
pressure is different, and by 10 steps later (my next output interval), 
all energy components as well as the pressure have diverged from those 
obtained for a run. This suggests that values used to calculate the 
total pressure (e.g. the virial) are not being preserved correctly 
across the restart, and this is subsequently perturbing the system, at 
least through the barostat.

However double precision gromacs performs "correctly" - all energy 
components and the total pressure are reproduced correctly in Step 0 of 
the restart, and future steps agree exactly (within output precision 
over only a few tens of MD steps) with those obtained from a run that 
extended over the restart time from the original starting point.

This suggests that something is being written or read at an 
inappropriate precision in the .edr files. Can this be brought to the 
attention of somebody who knows how that code is supposed to work, 
please? They may wish to see if they can reproduce my observations & 
work out what is wrong.

Mark
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Mark J. Abraham
Ph.D. Scholar
Computational Proteomics and Therapy Design Group
Division of Molecular Bioscience
John Curtin School of Medical Research
Australian National University
Canberra ACT 2601
Australia

Ph: 61-(0)2-6125 8305
Email:  Mark.Abraham at anu.edu.au
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