2012/11/2 <[email protected]>: > Hi Anu, > > I just have a few things to add: > > - after the first iteration, check the density profile after spline > smoothing in .smooth.dens (compare to the raw density file in .dist.new). If > there are oscillations, you have to tune the spline parameters. > - I am not sure postupd scale applies, but you can as well simply reduce the > prefactor to see if it is to high ( this may very well be if your CG model > has a different compressibility) Yes, postupd scale works as well, but out of all post update scripts scale and smooth are the only useful ones for the ft iteration.
Scaling the prefactor scales the forces (before integration) while postupd scale scales the potential (after spline fit and integration), so the result could be slightly different, but in principle it does the same. If you add the prefactor from the coarse-grained compressibility in cg_prefactor, a linear interpolation between cg_prefactor and the prefactor from the explicit compressibility will be used as a prefactor in the hybrid zone automatically. Christoph > - Increase the total simulation time per iteration step and trash some of > the trajectory in the beggining using gromacs.equi_time in the settings file > > Good luck! > > > -Sebastian > > Zitat von Christoph Junghans <[email protected]>: > >> Hi, >> >> 2012/10/31 Anu Nagarajan <[email protected]>: >>> >>> Hi, >>> >>> I am trying to run the thermodynamic force using csg_inverse. I have the >>> settings.xml file with appropriate options for my system. But, when I try >>> to >>> run TF, I get about 2-3 iterations after which the temperature gets >>> really >>> high and the system becomes unstable. I have the latest version (1.2.3) >>> of >>> votca. I computed the prefactor based on the compressibility of the >>> atomistic region. According to the tutorial and the paper, I have set >>> the >>> TF range to be d(skin)+d(at)+d(hy)+d(skin) where d(skin) is right now >>> half >>> the cutoff distance. The entire molecule is one charge group and I have >>> 12 >>> atoms plus virtual site. Do I have to change any values in the >>> settings.xml >>> file? Is there anything I might be missing? >> >> The parameters will depend on the system you study. >> Here are some things you could try: >> - increase adress_ex_forcecap in the mdp file >> - increase the spline grid (spline_start, spline_end in >> cg.non-bonded.inverse.tf) in setting.xml >> - add a cg_prefactor in cg.non-bonded.inverse.tf, which is based on >> the compressibility of the cg model >> - scale the update (add postupd task scale) by something < 1 >> >> Sebastian, please add stuff if I have missed something. >> >> Christoph >>> >>> >>> I appreciate any help in this matter! >>> >>> Thanks! >>> Anu >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca" group. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]. >>> For more options, visit this group at >>> http://groups.google.com/group/votca?hl=en. >> >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/votca?hl=en. >> >> >> -- >> This email was Anti Virus checked by Astaro Security Gateway. >> http://www.astaro.com > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
