Hi there, I am also doing FEP calculations and I am also using sd as integrator. The problem that I am having with this integrator is the temperature coupling (NTP). I am setting the targeted temperature of the system on 300K, for 2 Groups, Protein_and_ligand and Solvent. g_energy gives me 303K 301K respectably. If I use the md and noose-hover thermostat the results are 300K for both groups. For that reason I was thinking on changing to md. But afther reading the post
http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html I think that I shuold stick on sd. The questions are If by trying sd with target temperature 298K and get 300K as a result, is the simulation valid? Fabian, If you use sd the temperature of your system is the wanted one? Thanks in advance Marcelino Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Fabian Casteblanco wrote: > > > Dear all, > > > > I was running free energy calculation for a drug molecule in solvent. > > > > First, > > > > For [coulomb + vdW] --> [vdW] , I used 'md' integrator > > > > For [vdW] --> [none], I was using 'md' but it required me to switch > > to 'sd' based on this error message: > > > > "WARNING: For proper sampling of the (nearly) decoupled state, > > stochastic dynamics should be used. " > > > > Is using sd really much more accurate? Is it best to use 'sd' for > > [coulomb + vdW] --> [vdW] as well? > > > > > > > > Yes. See, for instance, some of the commentary here: > > http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html > > There are other posts regarding this topic, but I don't have the time to pull > them up. > > -Justin > > > > Thank you. > > > > -- > > Best regards, > > > > Fabian F. Casteblanco > > Rutgers University -- > > Chemical Engineering PhD Student > > C: +908 917 0723 > > E: fabian.castebla...@gmail.com > > > > > > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
