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.
