Hey Victor, Thanks a lot for your reply. I now understand that when it seemed to freeze it was actually doing the spline fitting.
The problem with this particular system is that there are only 4 A particles in it. Hence the large block size. Do you have a suggesting for getting around this? Patrick On Wed, Nov 16, 2011 at 4:16 PM, Victor Ruehle <[email protected]> wrote: > Dear Patrick, > > how many A particles (is it peptide?) do you have in your system? It > might be that your block size is too big. We typically used something > of the order of 10. Also your splinegrid seems quite dense with 90 > grid points. Start with a stepsize of 0.09 (30 grid points) and > block_size of 5 just and work your way up to bigger blocks & finer > grids. Every block_size frames, there is a break for solving the least > squares problem. That can take quite a while with the direct solver > currently implemented, especially for big systems / large block size / > fine spline grid, so don't be suprised. > > If that doesn't help let me know and we can do further testing. > > Cheers, > Victor > > 2011/11/16 Patrick Kiley <[email protected]>: > > Dear All, > > > > I am using csg_fmatch to develop nonbonded potentials for a peptide in > > tip3p water. My trajectory is very large to ensure good sampling - > > 200 ns with frames saved at 1 ps intervals. I have used csg_stat to > > determine min/max values and the step size. I run csg_fmatch like > > this: > > csg_fmatch --top atomistic.tpr --options fmatch.xml --cg > > "water.xml;pep_map.xml" --trj traj.trr --nframes <number> > > > > I expect this command to result in the creation of a file called A1- > > A1.force (see settings file below). > > > > If number > frames_per_block (see settings below) then csg_fmatch > > fills up all the memory while processor usage goes to zero. It then > > just sits there with no output until I kill it. > > > > However, if number < frames_per_block, then csg_fmatch terminates > > normally, but with no output. > > > > In all cases there is no output . . . Can anyone advise me on how to > > fix this problem? > > > > my settings file looks like this: > > <cg> > > <!--fmatch section --> > > <fmatch> > > <!--Number of frames for block averaging --> > > <frames_per_block>1000</frames_per_block> > > <!--Constrained least squares?--> > > <constrainedLS>false</constrainedLS> > > </fmatch> > > <!-- example for a non-bonded interaction entry --> > > <non-bonded> > > <!-- name of the interaction --> > > <name>A1-A1</name> > > <type1>A1</type1> > > <type2>A1</type2> > > <!-- fmatch specific stuff --> > > <fmatch> > > <min>0.30</min> > > <max>3</max> > > <step>0.03</step> > > <out_step>0.005</out_step> > > </fmatch> > > </non-bonded> > > </cg> > > > > > > Kind regards, > > Patrick > > > > -- > > 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.
