eva.pluhar...@marge.uochb.cas.cz wrote:
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
========================================
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