On Thu, Feb 20, 2020 at 10:29 AM Ali Khodayari <[email protected]> wrote: > > Dears, > > > > I am trying to derive potentials for a CG cellobiose-water system. I am using > IBI. The non-bonded interactions are derived using the distributions taken > from csg_stat, and I am trying to use csg_boltzmann to get the potentials for > bonded interactions. > > > > As the simulations crash at the very first step of the iteration, I tried to > add the potentials one by one (first bonds, then angles, and at the end > dihedrals). > > > > An error which I face regularly is: > > > > A tabulated bond interaction table number 1 is out of the table range: r > > 0.501462, between table indices 501 and 502, table length 501 > > > > I believe this is due to high forces between atoms at some point, shooting > the atoms to distances higher than the table’s length. > > > > After solving the issues with the bonds and angles, I am now trying to get a > nice potential for the dihedrals in my system. Yet, the potentials for the > dihedrals always look very weird (see table_d1.xvg). Without including this > table, the simulations in gromacs at least run for 1000 steps (1ps), but > including this crashes the simulations at the very first step. I am using the > following commands for csg_boltzmann: > > > > csg_boltzmann --cg "cellobiose.xml;water.xml" --top md_at.tpr --trj md_at.trr > < boltzmann_cmds2 > > > > having Boltzmann_cmds as: > > > > tab set T 300 > > tab set smooth_pot 1 > > tab set n 101 > > tab dihedral_yrry.pot *:dihedral-YRRY:* > > q > > > > The output is already looking very strange (see dihedral_yyry.pot) > > Then I use the following commands to get the table: > > > > BOND_FILE=$"dihedral_yrry.pot" > > SETTINGS="convert_dihedral.xml" > > > > # cut bad sampled regions at the boundaries > > sed -e '1,33d' -e 's/$/ i/' $BOND_FILE | tac | sed -e '1,0d' | tac > > "$BOND_FILE.cut" > > > > csg_call table smooth "$BOND_FILE.cut" "$BOND_FILE.smooth" > > csg_resample --in "$BOND_FILE.smooth" --out "$BOND_FILE.refined" --grid > 0:0.001:3.135 > > csg_call table extrapolate --function quadratic --region left > "$BOND_FILE.refined" "$BOND_FILE.refined1" > > csg_call table extrapolate --function quadratic --region right > "$BOND_FILE.refined1" "$BOND_FILE.cur" > > csg_call --ia-type dihedral --ia-name dihedral --options $SETTINGS > convert_potential gromacs "$BOND_FILE.cur" table_d${2}.xvg > > > > and the .xml file looks like this: > > > > <cg> > > <bonded> > > <bondtype>dihedral</bondtype> > > <name>dihedral</name> > > <min>0</min> > > <max>3.1415</max> > > <step>0.001</step> > > <inverse> > > <gromacs> > > <table>table_d1.xvg</table> > > </gromacs> > > </inverse> > > </bonded> > > > > <inverse> > > <gromacs> > > <pot_max>1e6</pot_max> > > <table_end>3.1415</table_end> > > <min>0.0</min> > > <max>3.1415</max> > > <table_bins>0.004</table_bins> > > </gromacs> > > </inverse> > > </cg> > > > > I have tried to cut different edges of the potential, but they all seem not > logical to me, and moreover, cause the simulation to crash at the very > beginning. > > > > Would you please kindly let me know if I am doing something wrong and/or how > I can resolve this issue? All that looks pretty reasonable to me, we recently found a bug in dihedral potential conversion see: https://github.com/votca/csg/pull/500 but in general dihedral IBI is pretty still pretty experimental in IBI and we should most likely add a warning about that to the code. I, personally, have not worked with dihedral potentials enough to give any advice on this matter.
Christoph > > > > My best, > > Ali > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/003b01d5e813%2416be71a0%24443b54e0%24%40gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e4b2UfYXQY9yyvZZGWxxDgWgUotf6wbBRcaQdx4H_e5JA%40mail.gmail.com.
