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.
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?). 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 ? 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.
