Dear Patrick, ok, and what do you do with the water? If you only use the peptide, you should easily be able to user bigger block sizes. Just try and increase the value and check how long it runs.
Best, Victor 2011/11/16 Patrick Kiley <[email protected]>: > 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. > -- 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.
