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>? 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?) 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? 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). 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.
