2014/1/21 Jakub Krajniak <[email protected]>: > Hi all, > > I am playing with Votca from a couple of weeks to get the effective > potential of quite simple polymer system. > Mainly I have very short (4 beads) polymer that I want to coarse grained to > two beads. In total there > are 100 of 'chains' in the box. In the fine scale there are angle, bond and > dihedral potentials to define the structure > of those 'chains'. The fine-scale simulation are governed by the espressopp > that gave me the trajectory file. The > bond distribution, angles, dihedrals, fluctuations of temperature and total > energy seems fine so I assumed that > the fine-scale simulation is correct. > > On the CG level I have actually only the bond potential and the > intermolecular potential. That simulation is also running on the espressopp. > For the bond potential I have used the csg_boltzmann to get it. And here > comes the first question: > 1. What temperature should be set in the csg_boltzmann? For the fine-scale > simulation I am using temperature defined by (T/kB<epsilon>) and my kB=1.0; > Also what temperature should be set in the <kBT> tag for the <inverse>? csg_boltzmann has gromacs units hard-coded.
I would suggest to write out the potentials with standard normalization (no bond/angle correction) and to use awk (see previous post on the mailing list) or csg_inverse's script to create an initial potential: $ csg_call --options settings.xml --ia-name bond --ia-type bond prepare_single ibi (only available in VOTCA 1.3) > > Then by using the csg_stat I am getting the target distribution. Second > question is related to the cut-off. Basically I use the 2.5*sigma where > sigma > is the same as in the fine-scale simulation (3.93). > 2. Should I use the same value in the <max> tag for the non-bonded (I see > that the target distribution range is related to it) or it should be > adjusted > differently? (The same question for the potential, should it be cut-off on > the same distance?) max is the value up to which VOTCA does IBI. Use a value where the rdf is close to 1. (Some papers says use a min of the rdf.) I normally use different max values for different interactions. Depending on your simulation program you want to extend the table using the table_end option, but for Espresso++ this isn't needed as it can handle multiple cutoffs. > > 3. Initial configuration, I saw that there are two options. One is to start > the simulation in every step from the same initial configuration, second one > is to start from the configuration from previous step. What is the best > approach? It depends! If you are sure your system stays in one phase all the time, laststep is the better option as it make VOTCA use an initial configuration, which is most likely closer to equilibrium. On the other hand if you sample different phases it might be better to start from the same conservative configuration, for which the system does't explode, all the time. In both case the equilibration time (equi_time) has to chosen with care. For IBI "laststep" would be the more traditional choice. > > And the convergence, I have add <post_add>convergence</post_add> so that I > can measure the convergence. > 4. What should be the optimal case for the convergence? > What I am getting: (step_001: ~300, step_002: ~232, step_003: ~133) and then > suddenly for step_004 it is ~8000. > There was one step where the convergence was around 90.. but I run it for > 100 steps and I don't see convergence at all. > (I used the <initial_configuration>laststep option). It seems something went wrong here, have a look at the different distributions to see if one of them is completely off. If so, you might need to scale the update and/or introduce an update cycle in do_potential. Christoph > > Thanks for any advice! > > Best, Jakub > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
