Dear Users,
I am trying to run IBI. I have 5 type of beads: POL, NON, GLY, ACI, BAS
My setting.xml:
<cg>
<non-bonded>
<name>ACI-ACI</name>
<type1>ACI</type1>
<type2>ACI</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>ACI-ACI.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_ACI_ACI.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>ACI-BAS</name>
<type1>ACI</type1>
<type2>BAS</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>ACI-BAS.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_ACI_BAS.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>ACI-GLY</name>
<type1>ACI</type1>
<type2>GLY</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>ACI-GLY.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_ACI_GLY.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>ACI-NON</name>
<type1>ACI</type1>
<type2>NON</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>ACI-NON.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_ACI_NON.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>ACI-POL</name>
<type1>ACI</type1>
<type2>POL</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>ACI-POL.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_ACI_POL.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>BAS-BAS</name>
<type1>BAS</type1>
<type2>BAS</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>BAS-BAS.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_BAS_BAS.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>BAS-GLY</name>
<type1>BAS</type1>
<type2>GLY</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>BAS-GLY.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_BAS_GLY.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>GLY-GLY</name>
<type1>GLY</type1>
<type2>GLY</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>GLY-GLY.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_GLY_GLY.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>GLY-NON</name>
<type1>GLY</type1>
<type2>NON</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>GLY-NON.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_GLY_NON.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>GLY-POL</name>
<type1>GLY</type1>
<type2>POL</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>GLY-POL.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_GLY_POL.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>NON-BAS</name>
<type1>NON</type1>
<type2>BAS</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>NON-BAS.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_NON_BAS.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>NON-NON</name>
<type1>NON</type1>
<type2>NON</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>NON-NON.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_NON_NON.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>POL-BAS</name>
<type1>POL</type1>
<type2>BAS</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>POL-BAS.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_POL_BAS.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>POL-NON</name>
<type1>POL</type1>
<type2>NON</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>POL-NON.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_POL_NON.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>POL-POL</name>
<type1>POL</type1>
<type2>POL</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<target>POL-BAS.dist.new</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<table>table_POL_POL.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<inverse>
<!-- 300*0.00831451 gromacs units -->
<kBT>2.49435</kBT>
<program>gromacs</program>
<gromacs>
<equi_time>10</equi_time>
<table_bins>0.002</table_bins>
<pot_max>1000000</pot_max>
<table_end>3.0</table_end>
</gromacs>
<filelist>grompp.mdp topol.top table*xvg index.ndx</filelist>
<iterations_max>500</iterations_max>
<convergence_check>default</convergence_check>
<convergence_check_options>
<limit>0.001</limit>
<name_glob>*.conv</name_glob>
</convergence_check_options>
<method>ibi</method>
<log_file>inverse.log</log_file>
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
and my grompp.mdp
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 25000000 ; 50 ns
nstcomm = 100
nstcalcenergy = 100
nstxout = 0
nstvout = 0
nstenergy = 0
nstlog = 10000
nstxtcout = 100
energygrps = ACI BAS GLY NON POL
energygrp_table = ACI ACI ACI BAS ACI GLY ACI NON ACI POL BAS BAS
BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL NON POL POL
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = User
rcoulomb = 1.4
vdw_type = User
rvdw_switch = 1.0
rvdw = 1.4
tcoupl = V-rescale
tc_grps = Protein
tau_t = 0.1
ref_t = 300
pcoupl = no
gen_vel = yes
gen_temp = 300
gen_seed = -1
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_iter = 1
lincs_order = 4
I am getting an error: get_simulation_setting: could not fetch
table-extension from grompp.mdp and no default given, please add it in
there #
I have table.xvg with "zeros" as well as all the files.
Would you pelase advise?
Steven
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