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. 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