W dniu poniedziałek, 8 lipca 2013 14:39:49 UTC+1 użytkownik Christoph
Junghans napisał:
>
> 2013/7/8 <s.neu...@gmail.com <javascript:>>:
> > 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
> So you need to add the table-extension option to your mdp file.
> table-extension = 2.0
> should work for you.
>
Can you please help with my mdp settings. I set:
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
table-extension = 2.4 ; *its distance beyond the largest
cuttoff so should be 2.4 as 1.4 (cuttof) + 2.2 makes the table 3.8*
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
rlistlong = 1.4
coulombtype = User
rcoulomb = 1.4
vdw_type = User
rvdw_switch = 1.0
rvdw = 1.4
But then I get error that rvdw < the lenght of the table (3.8 nm) which
makes sense. If I then set up the rlistlong and rvdw to 3.8 mdrun gives an
error: "Tables in file table_ACI_ACI.xvg not long enough for cut-off:
should be at least 6.200000 nm"
Would you please advise? Tutorials are supported by older Gromacs versions
as none of those settings are in the mdp file.
Steven
>
> > #
> >
> > I have table.xvg with "zeros" as well as all the files.
> >
> > Would you pelase advise?
> >
> > Steven
> >
> >
> >
> >
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>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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