On Fri, Feb 21, 2020 at 3:43 AM Ali Khodayari <[email protected]> wrote: > > Dear Christoph, > > Thank you for your response. Shall I replace the new potential_to_gromacs.sh > with the one I already have? Yeah, just copy the new version over in your installation.
> > I have another question. Could it be because of the type of dihedral I chose > that the potential does not exhibit high peaks on the two ends? The thing > that does not show it good to me is that I have very low energies on the two > ends of the parabolic shape. I honestly don't know. > > How can I adjust the amplitude of the two sides? For some of the potentials I > see very large peaks of 50000 and for some only 100 after extrapolating the > two sides. I also tried diffent extrapolators for my potentials. The extrapolation is done by taking the average slope of last 3 valid points on each side and that sometimes over/underestimates the slope, but usually the extrapolated part of the potential doesn't really matter much (for bonds and angles at least). Christoph > > My regards, > Ali > > > > -----Original Message----- > From: [email protected] <[email protected]> On Behalf Of Christoph > Junghans > Sent: vrijdag 21 februari 2020 0:48 > To: [email protected] > Subject: Re: [votca] derivation of potentials for dihedral > > 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. > > -- > 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/001001d5e8a3%24ccee9a00%2466cbce00%24%40gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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