eva.pluhar...@marge.uochb.cas.cz wrote:
Hi Justin,
thank you for suggestion about changing the integrator, but I would like
to know why it is not possible to sample properly by md under these
circumstances.
1. Do you know any papers about sampling efficiency of systems with almost
or completely switched off particles? How does it depend on the kind of
thermostat or barostat?
I don't know about papers, but there are several relevant discussions in the
list archive, i.e.:
http://lists.gromacs.org/pipermail/gmx-users/2003-June/006054.html
2. Note, that you can switch off the LJ particle also by creating B
topology with sigma and epsilon equal to 0 in the .top file, not using
couple-moltype. Doing so, there is no warning, but these approaches are
equivalent. This seems like internal inconsistency in Gromacs.
Sorry, can't comment here. Topology manipulation is outdated as of version 4.0,
but I guess it still works. Maybe some checks need to be implemented in this
case. It certainly seems like there can be artifacts if other .mdp parameters
are not set properly.
-Justin
Thanks again for any hints.
Best,
Eva
Hello all,
I am trying calculate desolvation free energy of Na+ in water using
option
couple-moltype, not by creating B-topology in the .top file.
At first, I switched off coulombic interaction using:
couple-moltype = Na+
couple-lambda0 = vdw-q
couple-lambda1 = vdw
Then I tried to switch off LJ interaction using couple-lambda0 = vdw
and
couple-lambda1 = none, but obtained this warning:
WARNING 1 [file equil_NVT000.mdp, line 95]:
For proper sampling of the (nearly) decoupled state, stochastic
dynamics
should be used
This is strange, because my .mdp file has only 94 lines.
Regardless of the line number, the error message is pretty explicit - you
probably have "integrator = md" in your .mdp file when you should have
"integrator = sd."
-Justin
Thanks in advance for any help or suggestion.
Best,
Eva
For convenience, I am pasting weak coupling algorithm section and free
energy section from my .mdp file. The simulation was performed at
constant
volume using strong temperature coupling, since it was an equilibration
run.
; OPTIONS FOR WEAK COUPLING ALGORITHMS
Tcoupl = v-rescale
tc-grps = system
tau_t = 0.1
ref_t = 300
nsttcouple = 1
; Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda = 0
foreign_lambda = 0.1
sc-alpha = 0.7
sc-power = 1
sc-sigma = 0.3
nstdhdl = 10
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
couple-moltype = Na+
couple-lambda0 = vdw
couple-lambda1 = none
couple-intramol = no
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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