Dear Users:
Has anyone successfully run the free energy tutorial at
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
?
I just tried it and I get a segmentation fault immediately (see output at the
end of this post).
I get a segfault with both 4.6.3
I found the -multi version of that tutorial a bit temperamental...
Michael Shirts suggested that double precision is more reliable for
expanded ensemble. Hopefully he can chime in in a day or two.
Mark
On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Dear
Thank you Mark.
I actually found that it crashed wihout the -multi part (no hamiltonian
exchange).
The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl
ethanol.1.dhdl.xvg
If I use the double precision version, there is no segfault. That's a working
solution, but it is worrysome.
Just to be clear, is this the expanded ensemble version of the calculation?
On Thu, Sep 26, 2013 at 5:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
I found the -multi version of that tutorial a bit temperamental...
Michael Shirts suggested that double precision is more reliable for
My mistake I still get a segfault even when using double precision. (EM
doesn't help, nor does switching to Berendsen pressure coupling).
Note that I can stop the segfault when running at init-lambda-state = 0 if I
set:
couple-lambda0 = none
couple-lambda1 = none
No, this is not the expanded ensemble version. It's the initial Running the
calculation with Gromacs section straight out of
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
I get the segfault with a single run (at any of the 9 individual lambda values).
I thought I had just managed to solve the issue :)
If you look at the soft core parameters, there are two types listed --
one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power
are more stable with single precision calculations.
I have changed the files on the website to make the
And with this change, single is running fine as well.
This was a known issue, but was only documented in the expanded.mdp
files, which was an oversight. After this, I switched so the default
is less likely to cause problems. Because of some theory improvements
developed in the group in free
solvation free energy tutorial
Next message: [gmx-users] segfault when running the alchemistry.org ethanol
solvation free energy tutorial
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
And with this change, single is running fine as well.
This was a known issue, but was only documented
assitance Mark and Michael.
Chris.
-- original message --
Michael Shirts mrshirts at gmail.com
Fri Sep 27 00:41:17 CEST 2013
Previous message: [gmx-users] segfault when running the alchemistry.org
ethanol solvation free energy tutorial
Next message: [gmx-users] segfault when running
10 matches
Mail list logo
