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 to trajectory before applying any constraints, which effectively change the actual force acting on the atoms?
thanks sikandar On Thu, Mar 10, 2011 at 5:10 PM, Victor Ruehle <[email protected]> wrote: > 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. > > The coarse-grained forces are then calculated according to the mapping > weights in the cg molecule definition. > > Some things to consider: > - make sure you don't use constraints during simulation > - be sure what you are doing if not using a center of mass mapping > > For more details see the paper by Noid et al: > http://jcp.aip.org/resource/1/jcpsa6/v128/i24/p244114_s1 > > Cheers, > Victor > > 2011/3/10 Sikandar Mashayak <[email protected]>: > > Hi > > Force matching algorithm tries to solve the eqn. 2.20 in the manual. So > for > > given set of CG force parameters, how does it compute the forces on CG > site > > using full atomistic MD trajectory? > > To do that I usually perform mdrun -rerun with mdp and topology files > > designed for CG system. Is csg_fmatch doing the same? > > thanks > > sikandar > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group at > > http://groups.google.com/group/votca?hl=en. > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
