hey I got the newly uploaded 1.1.2 tar and it installed well...
thanks sikandar On Sun, Apr 3, 2011 at 11:17 PM, Sikandar Mashayak <[email protected]>wrote: > 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 >> >> >> >>> >>> > >> >> >> >>> >>> > -- >> >> 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