[gmx-users] Re: mdrun -rerun and box size bug not fixed?

[Michel Cuendet]

Dear all,

By reactivating the barostat as mentioned below, I managed to recover LJ 
energies within 0.1% for my test system, which was a box of 1136 waters. 
So I applied the same thing to my system of interest (a 605 residue 
protein with around 25000 waters). The only difference is that the run 
was done with PME, and the rerun is done with RF, so I cannot compare 
electrostatics. For the other energies I get a systematic bias with 
respect to the original run, for example :

   - LJ :  70 +-50 kJ/mol higher than original  (0.05% of total)
   - g96 bonds : 160 +-60 kJ/mol higher than original (2.44% of total)

These biases are very reproducible over many trajectories with this 
system. The LJ bias might be considered negligible as it is a small 
percentage of the total LJ energy. However, the g96 bond bias is 
surprising (bonds are present only in the protein). We expect that the 
inaccuracy of the xtc coordinates generates some random noise. But I 
don't understand how it could generate a systematic error of that 
magnitude (2.44%) ...

I tried to change different parameters to trace the origin of this bias 
:  version of gmx, platform, huge compressibility, turning off the 
thermostats (for the g96 bond part), etc... Only turning the constraints 
off influenced the results, yielding an even higher bias towards higher 
g96 energies (210 +-60 kJ/mol).

Have such inaccuracies been observed before with -rerun? Am I doing 
something wrong or is there no hope of recovering better energies with a 
rerun?

Thanks,
Michel


-------- Original Message --------
Subject: 	Re: mdrun -rerun and box size bug not fixed?
Date: 	Tue, 06 Nov 2007 14:12:29 +0100
From: 	Michel Cuendet <michel.cuendet at isb-sib.ch>
To: 	gmx-users at gromacs.org
References: 	<20071102152757.0FAFD2435D at xray.bmc.uu.se>

Hi,

I think I got it :-) Using gmx 3.3.1 with the same thermostat and 
barostat settings as the original run, I get the right LJ energies 
within 0.1%. I used tcoupl and pcoupl = "no" because I somehow 
remembered that thermostats could do weird things when rerunning (see 
the old thread : 
http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html )

But apparently the box is not reread form the trajectory if the pcoupl 
option is deactivated. It would be much safer for users if the 
appropriate options were automatically set when -rerun in invoked:

nstlist = 1
nstenergy = 1
NO rescaling of velocities
NO rescaling of box size
Do read the box sizes from the trajectory

Cheers,

Michel



==========================================================
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
www.isb-sib.ch/groups/Molecular_Modeling.htm
==========================================================






-- 

==========================================================
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
www.isb-sib.ch/groups/Molecular_Modeling.htm
==========================================================