Dear VOTCAers,
I try to obtain the bonded CG potentials from sd simulation of a single
chain in vacuum using the IBI method, for which the VOTCA-1.3-dev is
employed. In the options.xml file, no non-bonded part is defined.
Consequently, some errors come up as given below. How to deal with this
problem, please? Thanks a lot for any reply.
Best regards,
Chaofu Wu
error message:
# convergence_check_default.sh: No convergence file found!
# Have you added convergence to the postadd list of at least one
interaction?
# For details see the logfile /home/xiaowu759/Workshop/inverse.log
options.xml:
<cg>
<bonded>
<name>bond_AA</name>
<min>0.24</min>
<max>0.34</max>
<step>0.002</step>
<inverse>
<target>bond_AA.dist.tgt</target>
<gromacs>
table_b0.xvg
</gromacs>
</inverse>
</bonded>
<bonded>
<name>bond_AB</name>
<min>0.26</min>
<max>0.30</max>
<step>0.002</step>
<inverse>
<target>bond_AB.dist.tgt</target>
<gromacs>
table_b1.xvg
</gromacs>
</inverse>
</bonded>
<bonded>
<name>angle_AAA</name>
<min>1.2</min>
<max>3.1</max>
<step>0.02</step>
<inverse>
<target>angle_AAA.dist.tgt</target>
<gromacs>
table_a0.xvg
</gromacs>
</inverse>
</bonded>
<bonded>
<name>angle_AAB</name>
<min>1.2</min>
<max>3.1</max>
<step>0.02</step>
<inverse>
<target>angle_AAB.dist.tgt</target>
<gromacs>
table_a1.xvg
</gromacs>
</inverse>
</bonded>
<bonded>
<name>dihedral_AAAA</name>
<min>-3.1</min>
<max>3.1</max>
<step>0.02</step>
<inverse>
<target>dihedral_AAAA.dist.tgt</target>
<gromacs>
table_d0.xvg
</gromacs>
</inverse>
</bonded>
<bonded>
<name>dihedral_AAAB</name>
<min>-3.1</min>
<max>3.1</max>
<step>0.02</step>
<inverse>
<target>dihedral_AAAB.dist.tgt</target>
<gromacs>
table_d1.xvg
</gromacs>
</inverse>
</bonded>
<bonded>
<name>dihedral_BAAB</name>
<min>-3.1</min>
<max>3.1</max>
<step>0.02</step>
<inverse>
<target>dihedral_BAAB.dist.tgt</target>
<gromacs>
table_d2.xvg
</gromacs>
</inverse>
</bonded>
<inverse>
<kBT>4.157255</kBT>
<program>gromacs</program>
<gromacs>
<equi_time>10</equi_time>
<table_bins>0.002</table_bins>
<pot_max>1000000</pot_max>
<table_end>2.2</table_end>
</gromacs>
<map>map12.xml</map>
<filelist>grompp.mdp topol.top table.xvg index.ndx</filelist>
<iterations_max>10</iterations_max>
<convergence_check>
<type>default</type>
<limit>0.001</limit>
</convergence_check>
<method>ibi</method>
<log_file>inverse.log</log_file>
<restart_file>restart_points.log</restart_file>
</inverse>
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