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
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