Re: [votca] FM for Mixture

I am kinda confused here. Lets say I have mixture of two molecules, one with more than one atoms and second one is just simple one atom molecule, call it as CG1. Then I wish to coarse-grain multi-atom molecule to its COM site, call it as CG2 and now determine what is the effective CG potentials be

Re: [votca] Force Matching F_CG

Hey Victor Thanks for clarification. But I am worried about not using constraints during simulation. If my definition of molecule requires to apply constraint, like using Settle for SPC/E water, then how can I remove them. Also, why is this condition? Is it because that Gromacs writes the forces t

Re: [votca] FM for Mixture

Hey, how do you want do describe interactions between coarse-grained and atomistic molecules? Each atom with coarse-grained site? How many different atom types and with that interactions will you have then? Also be aware that mixing resolutions might lead to additional problems. Currently the onl

Re: [votca] Force Matching F_CG

Hey, VOTCA does not compute atomistic forces, they need to be provided in the atomistic trr file (just switch on writing forces in gromacs). You should do same output frequency for forces as for coordinates. So you can do it while running or use rerun to calculate forces for an existing trajectory

Re: [votca] Re: Votca 1.1 announcement

Am 03/10/2011 04:14 AM, schrieb Sikandar Mashayak: Is thread options available for csg_fmatch? If yes, how can I use that? At this point only csg_stat is using threads, but we are working on that (see issue 82, ). Feel free to contribute the