Dear Justin, Thanks for your reply. You said "....You should avoid ad hoc changes." You used different parameters for energy minimization at tutorial called "Tutorial 5: Protein-Ligand Complex". *a part of your em.mdp* nstlist = 1 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 *a part of your md.mdp* nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4
Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for energy minimization? Thanks in advance 23 Mart 2012 19:31 tarihinde Justin A. Lemkul <jalem...@vt.edu> yazdı: > > > ahmet yıldırım wrote: > >> Dear users, >> >> I am using the Reaction-Field method for electrostatics interactions. I >> used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, >> npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set >> nstlist=rlist=rcoulomb=rvdw=1.**0 for energy minimization, would not it >> be better? What is your suggestions? >> >> > Why do you think making such changes to the cutoffs would be better? > These settings, for the most part, are a fixed part of the force field > you're using. Unless you have proof (either by your own demonstration or > one that is published) that making such changes result in better results, > you should avoid ad hoc changes. > > ; Neighbor Searching Parameters >> nstlist = 5 ns-type = Grid pbc >> = xyz rlist = 0.9 ; >> Electrostatics >> coulombtype = Reaction-Field rcoulomb = 1.4 >> epsilon_rf = 54 ; VdW >> vdw-type = Cut-off rvdw = 1.4 >> * >> Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, >> npt.mdp and md.mdp) the reference temperature for coupling. I analysed the >> temperature after production run. I get "Temperature=312.646" (g_energy -f >> md.edr -o temperature.xvg). that is, The temperature has increased >> (approximately 12 K) during the simulation. What could be the reason for >> the increase in temperature? I had setted to 200 K the reference >> temperature for coupling in pr.mdp. it can cause? >> >> > This outcome is precisely what you would expect, simply because you're > using the reaction field method and it introduces cutoff artifacts. > Interestingly, this same outcome (an increase of exactly 12K) has been > reported before: > > http://lists.gromacs.org/**pipermail/gmx-users/2009-**January/039113.html<http://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html> > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım
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