if i understood correctly what you mean with error force (=force difference) then yes.
I made changes and options should be available now. Please reinstall csg (either stable or developer version from repositories). Tarballs are not yet updated. I'm not aware of any gromacs tool which does it. However that would be a perfect exercise to get startet with votca development :) It's 3 additional lines in the template.cc. I can help you to get started. Victor 2011/4/1 Sikandar Mashayak <[email protected]>: > yeah sure it helps.. just to be sure that I understand it correctly > when --traj ref.trr --trj-force cg.trr is used with csg_fmatch then it > computes the difference between forces on cg site in ref.trr and cg.trr and > use error forces as a target force to be matched using the CG potentials > with given options.. > right? > also, is there any gromacs utility can be used to compute force difference > between two .trr with same positions and generate new .trr with error > force? > thanks > sikandar > > On Thu, Mar 31, 2011 at 4:09 PM, Victor Ruehle <[email protected]> wrote: >> >> 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. >> > > -- > 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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