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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