[gmx-users] free energy calculation
mgoette at mpi-bpc.mpg.de
Mon Jan 29 16:59:15 CET 2007
You are probably starting your runs from a non equilibrated structure.
Assume, the system changes via a slow growth run.
The atoms may rearrange due to changes in their potentials.
Therefore it may be problematic, if you start from the same structure
for different lambdas. Try simulating a one way slow growth and pick the
snapshots close to your lambda value from the trajectory and start your
"quasi-FEP" with those.
I can't answer your second question properly, because I don't know the
code itself. But my guess is, that GROMACS calculates the potential for
state A and B and then interpolates between them in a linear fashion
(dependent of if you use soft-core or not). From this arises a yes for
the second part of your question. If I'm wrong with that, I'm sure,
someone who knows better will correct me quite fast. ;)
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Paolo Cerri wrote:
> Dear all,
> I'm trying to calculate free energy differences using the standard
> method of thermodynamic integration.I calculate dG/dlambda for different
> values of lambda and then integrate.
> When decoupling LJ interactions i have LINCS WARNING:
> Step 1, time 0.002 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.007366 (between atoms 7 and 8) rms 0.002535
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 7 8 50.1 0.1010 0.1017 0.1010
> 9 10 65.8 0.1090 0.1085 0.1090
> 17 18 32.1 0.1010 0.1011 0.1010
> 17 19 32.0 0.1010 0.1011 0.1010
> and eventually the simulation stops (during the equlibration run at
> lambda >= 0.9)
> I obtain the following message:
> Program mdrun, VERSION 3.3.1
> Source code file: clincs.c, line: 559
> Fatal error:
> Too many LINCS warnings (10001) - aborting to avoid logfile runaway.
> This normally happens when your system is not sufficiently
> equilibrated,or if you are changing lambda too fast in free energy
> simulations.If you know what you are doing you can adjust the lincs
> warning threshold
> in your mdp file, but normally it is better to fix the problem.
> I remark that in my simulations lambda is not changed continuously
> during simulation, but i perform several simulations at different fixed
> lambda values.
> I change only LJ interactions (having previusly turned of Coulomb
> I use Amber forcefield ffamber99
> thanks in advance
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