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.
