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 <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
References: <[EMAIL PROTECTED]>
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
==========================================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
