2013/3/15 <[email protected]>: > Thank you for this. > > I tried csg_boltmann and got potentials and distributions for my bonds and > angles. I tried to compare those distributions with those obtained by > Gromacs using g_rdf -rdf mol_com > and the equilibrium distance (maximum of distributions on x axis) lies in > the same place but distribution obtained from gromacs is thousands times > taller. Could you please explain this? I guess, this is just a normalization issue. We calculate the distribution P , not the histogram H. Their relation ship is: P(r)= H(r) / (4*pi*r^2) > > Can csg_boltmann do dihedrals as well? Or would you recomment g_stat for > this? Yes, you can. You have to create a dihedral block (like the bond and angle block) in the cg_bonded part of the mapping file, see the manual for details.
Christoph > > Steven > > W dniu piątek, 8 marca 2013 17:21:31 UTC użytkownik Christoph Junghans > napisał: >> >> 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. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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