Hi Anu,
in case you have oscillations, it is actually more appropriate to decrease spline_step parameter, which will make the spline 'less stiff'. Good luck! -Sebastian > Hi Christoph and Sebastian, > > I have tried all the options with no luck. The compressibility of CG > is different than the EX so I tried adding the cg_prefactor. But this > hasn't improved the number of cycles. > > When comparing the densities like Sebastian suggested, I found that > there were oscillations so I have increased the spline length. That > hasn't helped either. The spline max right now is equal to the box > length. > > I have increased ex_force_cap, played around with spline values and > equi_time. Is there anything else I can try? > > Thanks a lot! > > Anu > > On Fri, Nov 2, 2012 at 11:32 AM, Christoph Junghans > <[email protected] <mailto:[email protected]>> wrote: > > 2012/11/2 <[email protected] > <mailto:[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] > <mailto:[email protected]>>: > > > >> Hi, > >> > >> 2012/10/31 Anu Nagarajan <[email protected] > <mailto:[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 <http://cg.non-bonded.inverse.tf>) in > setting.xml > >> - add a cg_prefactor in cg.non-bonded.inverse.tf > <http://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] > <mailto:[email protected]>. > >>> To unsubscribe from this group, send email to > >>> [email protected] > <mailto:votca%[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] > <mailto:[email protected]>. > >> To unsubscribe from this group, send email to > >> [email protected] > <mailto:votca%[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] > <mailto:[email protected]>. > > To unsubscribe from this group, send email to > > [email protected] > <mailto:votca%[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] > <mailto:[email protected]>. > To unsubscribe from this group, send email to > [email protected] > <mailto:votca%[email protected]>. > For more options, visit this group at > 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. -- You received this message because you are subscribed to the Google Groups "votca" group. 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