Dear VOTCA users,
I am trying to calculate the other bonded distributions that I did not
iterate over during each iteration. I am iterating over the angle term only
but I want to see how the bond and dihedral terms change. I just want to
calculate the bond and dihedral distribution without iterating or producing
potential for them.
I used the following example, but I still produce potential for bond and
dihedral. I think because I included "<inverse> </inverse>"
<cg>
<bonded>
<!-- bond -->
<name>bond1</name>
<min>0.236000</min>
<max>0.292000</max>
<step>0.001</step>
<inverse>
<target>bond1.dist.tgt</target>
<gromacs>
<table>table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- angle -->
<name>angle1</name>
<min>1.100175</min>
<max>1.801287</max>
<step>0.001</step>
<inverse>
<target>angle1.dist.tgt</target>
<do_potential>1</do_potential>
<post_update>scale</post_update>
<post_update_options>
<scale>0.010000</scale>
</post_update_options>
<post_add>convergence</post_add>
<gromacs>
<table>table_a1.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- dihedral -->
<name>dihedral1</name>
<min>-1.510723</min>
<max>2.801333</max>
<step>0.01</step>
<inverse>
<target>dihedral1.dist.tgt</target>
<gromacs>
<table>table_d1.xvg</table>
</gromacs>
</inverse>
</bonded>
<inverse>
<kBT>2.49435</kBT>
<program>gromacs</program>
<gromacs>
<equi_time>200</equi_time>
<table_bins>0.002</table_bins>
<pot_max>1000000</pot_max>
<table_end>5.0</table_end>
<topol>topol.tpr</topol>
<traj>traj.xtc</traj>
<mdrun>
<opts> -nt 4 </opts>
</mdrun>
</gromacs>
<map>NCP_CG.xml</map>
<filelist>grompp.mdp topol.top table.xvg index.ndx table_b1.xvg
table_d1.xvg </filelist>
<iterations_max>1</iterations_max>
<convergence_check>
<type>default</type>
<limit>5</limit>
</convergence_check>
<method>ibi</method>
<log_file>inverse.log</log_file>
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
Thanks
Mohammad
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