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. ;)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.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
interactions)
I use Amber forcefield ffamber99
thanks in advance
Paolo
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