Hey I may need a bit more explanation to understand last two points you make..
*- csg_fmatch --trj traj.trr --force-trj traj_rerun_cg.trr (fill give* *error force)* * * *::-* will the output of this be .trr file with error forces or CG potential which reproduces error forces. Also I don't see the --force-trj option in help text/manual for csg_fmatch. *You could test whether you did it correct be using force-matching* *potentials as input for rerun -> error force should vanish* * * This point is not clear. thanks sikandar On Thu, Mar 31, 2011 at 11:19 AM, Victor Ruehle <[email protected]> wrote: > Hey > > unless you change your basis set for cg force field (cut-off, add > interactions, etc) or add some bias to fit procedure (extension to > code needed), you will probably end up with identical potentials as > doing only force matching. > > However, technically it can be done the following: > - csg_map --in traj.trr --out traj_cg.trr --cg mapping.xml (same for > conf.gro) > - prepare coarse-grained topolology with already known potentials > - mdrun -rerun traj_cg.trr (trajectory will contain knowledge based > forces) > - csg_fmatch --trj traj.trr --force-trj traj_rerun_cg.trr (fill give > error force) > > You could test whether you did it correct be using force-matching > potentials as input for rerun -> error force should vanish > > Victor > > 2011/3/31 Sikandar Mashayak <[email protected]>: > > Hi > > Another similar situation I am thinking of is like follow :: > > 1. I have full atomistic trajectory and forces as a target system. > > 2. I want to Coarse-Grain and determine CG-CG potential. I also have some > > knowledge what this CG-CG looks like and and insist on using this > > information. To do that I plan to do following. > > 3. Use this knowledge based ( so to call) CG-CG to perform MD-Rerun with > > full atomistic trajectories and get CG forces. > > 4. Now compute the error in forces on CG site for full MD and CG > MD-rerun. > > 5. Use this error force as target force to do Force-Matching and get an > > estimate for CG-CG potential which reproduces this error. > > 6. Finally add this error CG potential to original (knowledge based) > > potential to get more accurate CG-CG potential. > > > > So the question I have is, how do I generate trajectories for just error > > forces. I mean , is there any way I use two gromacs trajectories and get > new > > trajectory with error force? > > thanks > > sikandar > > > > On Mon, Mar 28, 2011 at 5:35 PM, Sikandar Mashayak <[email protected] > > > > wrote: > >> > >> thanks victor, I will see how subtracting known parts and setting > interval > >> to the unknown range will work out.. i guess good starting point would > be > >> check this out with simple 12-6 LJ case... > >> --- > >> sikandar > >> > >> On Wed, Mar 23, 2011 at 6:13 PM, Victor Ruehle <[email protected]> > wrote: > >>> > >>> Hmm, don't see any clean way how to do this with the current > >>> implementation. One might be able to subtract the known parts (which > >>> can be calculated using rerun) using --force-trj and setting the > >>> interval only to the unknown region. However this might lead to kinks > >>> due to interpolation effects at the crossing. > >>> > >>> The clean way would require extending the code. > >>> > >>> 2011/3/15 Sikandar Mashayak <[email protected]>: > >>> > Hey > >>> > I am thinking of a problem where I have some physical understanding > or > >>> > constraint for CG-CG potential that I want to parameterize. So that, > I > >>> > know > >>> > say from 0-r1 what is CG-CG potential values and want to determine > >>> > values > >>> > from r1-rcut. > >>> > Is there any way I can set up such Force Matching calculations in > >>> > Votca? > >>> > 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. > > > > -- > 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. 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