Hey Victor I was able to use template.c to write out new trr with error forces. Also, it may be useful for me to modify csg_map to generate output trajectory in .trr format with force information, I will give it a try whenever possible. Right now, as I said earlier, I need to do fmatch on error forces. As you suggested, I am trying to use *"--trj-force" *option to accomplish that. But when I try to download updated csg source code and compile it I get the errors. I have attached the build log file . Can you please help me with that
thanks sikandar On Sat, Apr 2, 2011 at 2:10 AM, Victor Ruehle <[email protected]> wrote: > Check e.g. in csg_map.cc > (http://doxygen.votca.googlecode.com/hg/csg__map_8cc_source.html) > > string out = "foo.trr"; > _writer = TrjWriterFactory().Create(out); > if(_writer == NULL) > throw runtime_error("output format not supported: " + out); > _writer->Open(out); > _writer->Write(top); > _writer->Close(); > delete _writer; > > You can access topology class to make changes > (http://doxygen.votca.googlecode.com/hg/classvotca_1_1csg_1_1Topology.html > ) > > 2011/4/2 Sikandar Mashayak <[email protected]>: > > yeah, I have been using template.cc for doing post-processing the > > trajectories, but I am used to writing the analyzed data in ascii format, > > not sure how to generate .trr format files with modified data... looking > > into xtc gromacs library... your input on this will be helpful... > > thanks > > sikandar > > > > On Fri, Apr 1, 2011 at 5:20 PM, Victor Ruehle <[email protected]> wrote: > >> > >> 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 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csg_build.log
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