2013/3/8 <[email protected]>: > > > W dniu poniedziałek, 4 marca 2013 18:02:23 UTC użytkownik Christoph Junghans > napisał: >> >> Hi Steven, >> >> 2013/3/4 <[email protected]>: >> > Dear Votca Users, >> > >> > I am new to the software. I tried some tutorials but many things are >> > still >> > not clear for me as my system is slightly more complex. >> Welcome. > > > Thank you for your prompt reply. > >> >> > >> > My atomistic simulation is one trimer of 3 amino acids in TIP3P water >> > model. >> > What I want to extract is just the bonded parameters by IBI between 3 >> > beads >> > ech represented by amino acid. >> > >> > So the key is the tabulated potential of two bonded interactions and one >> > angle. My questions: >> > >> > Does my reference simulation (atomistic) obtained by Gromacs should have >> > [ >> > exlusions ] of non-bonded parameters so the potentials will be given >> > only >> > for bonded? Shall I include in my mdp file while performing atomistic: >> > energy_grps so I can use g_energy then to see the bonded potential? I >> > know >> > VOTCA does this but not sure based on what kind of trajectory (with >> > excluded >> > nonbonded?). >> Basically there are two strategies to obtain coarse-grained potential >> for bonded interactions. >> 1.) Separation of bonded and non-bonded. (see Tschoep et al. Acta >> Polymerica 49, 61 (1998).) >> - run the molecule in vacuum (without solvent) and exclude all >> interaction, which are later covered by non-bonded interactions. >> - use simple Boltzmann inversion to obtain the bonded interaction (use >> csg_stat/awk or csg_boltzmann for that) > > > Shall include [ exclusions ] in my atomistic simulation on vacuum of all > atoms from the desired 1st bead with atoms from the 2nd and 3rd bead + > exlclusions of atoms of the 2nd bead with atms of the 3rd? Or its better to > group atoms in my index file in GMX - Bead1, Bead2, Bead3 and then > in my mdp run: > energygrp-excl = Bead1 Bead2 Bead1 Bead3 Bead2 Bead3 Energy group exclusions are on top of the topology, Gromacs has another loop over all pairs of energy group. And because they are not part of the molecular topology, VOTCA don't know about them.
But these exclusion would only matter if you calculate distribution for atomic (unmapped) coordinated using csg_stat As long the bead were somehow excluded during atomistic simulation and are excluded after the mapping (csg_dump --cg --excl ) everything should be fine. > ?? How do you personally do it? I usually put things in [exclusion], but that is more my personal preference. Gromacs gets slower the more energy group you have, but that is not so important for a single molecule in vacuum. > >> - obtain the other interaction by IBI of a cg simulation with the >> above bonded interactions fixed (use csg_inverse) >> 2.) Do IBI on all interaction (use csg_inverse) >> - due to our lazyness in the implementation, you will also need >> initial guesses for the bonded table here as well and hence you have >> to the 2nd step of 1.). >> >> If 1.) or 2.) is better depends a bit on how stiff your bonded >> interactions are and hence how good the separation works > > > In this case I think it is good to do the step 1 and then the table of > bonded can be an input to the second one so results will be more realistic. > Am I right? In 2.) the tables for the bonded interaction are used as initial guesses, an IBI update will still be applied on these, but it always good to try 1.) first as it saves you a lot of time and work if it works. > > >> >> >> Concerning the exclusions, all VOTCA programs tolerate the exclusion >> given in the tpr file if you don't map. >> If you map first, VOTCA generates its own exclusion, which basically >> mean every pair which is connected by a bonded interaction (specified >> in the mapping file) is excluded. In both cases, exclusions can be >> check using csg_dump --excl (together with --cg for mapped >> trajectories). >> >> > >> > Presuming I got my 3 bonded potentials (table.xvg). Shall i use in my CG >> > run: >> > >> > mdrun -v -tablep tablep1.xvg tablep2.xvg -tablea tablea.xvg -deffnm md >> > >> > How Gromacs know which potential belong to which bond? Isnt it easier to >> > fit >> > the curve into the parabolic shape and extract both equilibrium >> > distance/angle and the force constant adding to ffbonded.itp ? >> Gromacs has a naming scheme for its tables. >> For bonded tables: >> <TRUNC>_<A,B or D><NR>.xvg >> and for non-bonded tables: >> <TRUNC>_<E1><_E2>.xvg >> >> TRUNC is determined by the -table (nonbonded) and -tableb (bonded) >> options. >> E1,E2 are energy groups >> A,B,D stands for angle, bond, dihedral >> NR is the integer you specify in 4th column for of the bonds or angles >> block in the top file. >> For example >> [ angles ] >> ; ai aj ak funct NR k >> 1 2 3 8 1 1.0 >> (k ist another scale factor) >> >> I normally just use the default naming convention (mdrun without >> -table options), which lead to table names like >> table_A_B.xvg, table_b1.xvg and table_b1.xvg. >> >> Christoph >> >> > >> > I am sorry for basic questions but it is not clear to me. >> > >> > Thanks, >> > >> > >> > Steven >> > >> > >> > >> > -- >> > 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?hl=en. >> > 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?hl=en. > 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
