Dear Christoph and Sebastian, Thank you for your suggestions! I will try them out and let you know how it goes.
Anu On Fri, Nov 2, 2012 at 6:07 AM, <[email protected]> wrote: > 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) > - 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 >>> votca+unsubscribe@**googlegroups.com<votca%[email protected]> >>> . >>> For more options, visit this group at >>> http://groups.google.com/**group/votca?hl=en<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 votca+unsubscribe@** >> googlegroups.com <votca%[email protected]>. >> For more options, visit this group at http://groups.google.com/** >> group/votca?hl=en <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 votca+unsubscribe@** > googlegroups.com <votca%[email protected]>. > For more options, visit this group at http://groups.google.com/** > group/votca?hl=en <http://groups.google.com/group/votca?hl=en>. > > -- 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.
