sorry, sure it is --trj. This will generate a mapped trajectory. Then you have to calculate forces using gromacs mdrun -rerun giving a coarse-grained topology which contains forces you already know. To summarize -> csg_map will generate a coarse-grained trajectory from atomistic one (only positions), mdrun -rerun adds forces
on csg_fmatch --trj-force (mixed it up --force-trj was wrong): indeed, it seems like i forgot to merge that into the stable/default branch. Will fix it by tomorrow and let you know when done. on testing: With --trj-force you can specify a coarse-grained trajectory whose forces are subtracted before force fitting procedure. If you now put in the potentials obtained in a previous forcematching step, these are subtracted -> the forces which are fitted should be zero (the fit depends on specified interactions, if you don't change these it should give identical results, since these are already subtracted -> zero). This is good to check whether your setup of coarse-grained topology is correct (interactions specified correctly) and all steps I mentioned went fine. Hope that helped. Cheers, Victor 2011/3/31 Sikandar Mashayak <[email protected]>: > Also, when running the command > csg_map --in traj.trr --out traj_cg.trr --cg mapping.xml > i get error " unknown option --in" and when I do it usual way i.e. csg_map > --top top.tpr --traj traj.trr --out out.trr I get the .trr file but it has > zero forces/no force information. > > > On Thu, Mar 31, 2011 at 11:38 AM, Sikandar Mashayak <[email protected]> > wrote: >> >> 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. > 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.
