Dear Gromacs users,<br><br> One example of my mdp files with lambda=0.5 is like the following:<br><br>integrator = md<br>tinit = 0<br>dt = 0.004<br>nsteps = 250000<br>
simulation_part = 1<br>comm_mode = Linear<br>nstcomm = 10<br><br><br>nstlist = 2<br>ns_type = grid<br>pbc = xyz<br>periodic_molecules = no<br>
rlist = 1.4<br><br><br>coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 1.4<br>epsilon_r = 1<br>epsilon_rf = 1<br>vdw_type = cut-off<br>
rvdw = 1.4<br>fourierspacing = 0.168<br>pmeorder = 4<br>ewald_rtol = 1.0e-5<br>ewald_geometry = 3d<br>optimize_fft = yes<br><br><br>tcoupl = v-rescale<br>
tc-grps = ioq !ioq<br>tau_t = 0.1 0.1<br>ref_t = 298.15 298.15<br>pcoupl = Berendsen<br>Pcoupltype = Isotropic<br>tau_p = 1.0<br>
compressibility = 4.5e-5<br>ref_p = 1.0<br><br><br>constraints = all-bonds<br>constraint_algorithm = lincs<br>lincs_order = 4<br>lincs_iter = 1<br><br>
free_energy = yes<br>init_lambda = 0.5<br>delta_lambda = 0<br>foreign_lambda = <br>sc-alpha = 0.7<br>sc-power = 1<br>sc-sigma = 0.3<br>
nstdhdl = 10<br>separate-dhdl-file = yes<br>dhdl-derivatives = yes<br>dh_hist_size = 0<br>dh_hist_spacing = 0.1<br>couple-moltype = <br>couple-lambda0 = vdw-q<br>
couple-lambda1 = vdw-q<br>couple-intramol = no<br><br> The system has 1 Chloride ion with ffG43a1 force field parameter and SPC water molecules with heavy hydrogen in a cubic box of size 3 nm. I have sampled 21 lambda windows ranging from 0 to 1.<br>
<br> The values are converged by block averaging. <br><br> Regards,<br> Yan<br><br><div class="gmail_quote">On Thu, Apr 14, 2011 at 3:35 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Yan:<br>
<br>
If you want to get to the bottom of this then (a) please report your mdp files and (b) show some evidence that your values are converged by, for instance, block averaging the run-time.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Dear Gromacs users,<br>
<br>
I got different free energy values by Thermodynamic Integration (TI) in<br>
Gromacs 4.0.7 and 4.5.3.<br>
<br>
When I calculated the hydration free energy of Chloride ion by using<br>
Thermodynamic Integration method, the results for the free energy of<br>
un-charging the Chloride ion from q=-e to 0 in SPC water are 359+/-6 kJ/mol<br>
in Gromacs 4.0.7 and 385 +/-6 kJ/mol in Gromacs 4.5.3, respectively.<br>
<br>
The literature value is 392 kJ/mol (J. Phys. Chem. 1996, 100, 1206-1215,<br>
Table 6), which is close to the result in Gromacs 4.5.3 but not in 4.0.7.<br>
<br>
As a check, Gromacs 3.3.1 gave the result as 381+/-3 kJ/mol.<br>
<br>
I searched the mail list and the bugzilla of Gromacs but didn't find<br>
explanation for this issue of version.<br>
<br>
Does anyone know the reason for the different TI free energy values in<br>
those different version of Gromacs?<br><font color="#888888">
<br>
-- <br>
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</font></blockquote></div><br>