On Wed, Aug 19, 2020 at 4:44 AM Pragati Sharma <[email protected]> wrote: > > > Hello all, I solved the topology mismatch issue and my CG simulation is now > running. > But I am still struggling to understand the values I got in table_nonbonded > entries ike this: > > 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 > 0.0000000000e+00 1.3613480400e+04 0.0000000000e+00 > 2.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 > 0.0000000000e+00 1.3051740430e+04 2.7608764250e+05 > 4.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 > 0.0000000000e+00 1.2509129830e+04 2.6620522750e+05 > 6.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 > 0.0000000000e+00 1.1986919520e+04 2.5568735500e+05 > 8.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 > 0.0000000000e+00 1.1486380410e+04 2.4453402500e+05 > 1.0000000000e-02 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 > 0.0000000000e+00 1.1008783420e+04 2.3375991250e+05 > 1.2000000000e-02 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 > 0.0000000000e+00 1.0551340760e+04 2.2442411500e+05 > There are seven columns, e.g in table_A_A.xvgfile. What are these entries > for? Which one represents potential. See section 5.8.12 of the gromacs manual: http://manual.gromacs.org/2019/manual-2019.pdf In short, VOTCA stores the potentials in a files called <name>.pot.cur and then converts in to an xvg file for gromacs. The xvg file has seven columns for x(=distance0, colomb, coulomb forces,C6, C6 forces C12 and C12 forces. VOTCA uses the C12 part instead of the C6 or a mixture.
Christoph > > Thanks in advance. > > > ---------- Forwarded message --------- > From: Pragati Sharma <[email protected]> > Date: Wed, Aug 19, 2020 at 12:34 PM > Subject: Re: [votca] Re: IBI error: segmentation fault at csg_inverse step of > IBI in step001 > To: <[email protected]> > > > Thanks Christoph. I can solve the segmentation fault and simulation runs for > 1 step, however it does not go to second step and stops with below error: > > "Topology does not have beads of type "C" > This was specified in type1 of interaction "C-C" > > If there is any problem with topology, it should not run the first step also. > Is there any issue with the molecule names??? Because it also says a warning: > WARNING: unknown molecule "CGBUT" with id 1 in topology > I am attaching the two coarse grained topology files and inverse.log file and > mdp file also. > > Along with this problem, the tabulated potentials for non-bonded interactions > generated in step 1 gives all values as zero. Why is it?? Is it because I am > not using exclusions? > > Thanks in advance. > > On Thu, Aug 6, 2020 at 9:06 PM Christoph Junghans <[email protected]> wrote: >> >> On Wed, Aug 5, 2020 at 9:04 PM Pragati Sharma <[email protected]> wrote: >> > >> > >> > It is the mdrun command, where the error comes. I have attached the >> > inverse.log file here also. Thanks. >> That usually means your system exploded, maybe there is a message from >> mdrun in one of the log files as well. >> The reason for that is most likely that one of the bonded interactions >> is screwed up. >> You could try to run it with harmonic interactions as a start to check that. >> >> Christoph >> > >> > >> > >> > >> > On Wednesday, 5 August 2020 17:15:42 UTC+5:30, Pragati Sharma wrote: >> >> >> >> Dear all, >> >> >> >> I am trying to run CG simulations of 5mer-polybutadiene using IBI method >> >> and following hexane tutorial. >> >> I am getting segmentation fault at step 1, when I run csg_inverse command. >> >> Below are the steps I followed and files attached. Please guide me >> >> towards the probable reason of the error. >> >> >> >> 1. csg_mapp and csg_gmxtopol " generate cg.gro and cg.top >> >> >> >> 2.Run run_Boltzman.sh script to get target distributions and potentials >> >> (This gives tabulated potential files for bonded interactions only) >> >> >> >> 3. Run run.sh script (for getting non-bonded potentials): I provide the >> >> tabulated bonded potentials obtained in step 2 here for simulation and >> >> run csg_inverse. In this step the error comes. >> >> >> >> Sometimes the error shows infinite potential energy in the system. >> >> >> >> I guess there is some issue with my bonded potentials. I have read you >> >> have to "manually delete poorly sampled parts" from potential files. How >> >> to do it, If that is the reason. >> >> >> >> I am attaching the potential files here. >> >> >> >> Thanks >> >> >> >> >> >> >> >> >> >> >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > 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/3a89f8a1-74ba-4942-9581-5bb248b77ceco%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> 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/CAHG27e7P4MsEtBBcj2iRiUQOLSwBEbyOVShSt65uxfu1gNEZuQ%40mail.gmail.com. > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > 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/CAMpF9Q3Qm9AEffepfET-_RPpXMjzeV%2BU224byE10Edma6-a5BA%40mail.gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- 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/CAHG27e4ta31XxAV_hxvGN08CVKfDkH6qv_nfojWo_fr%2BxXiQew%40mail.gmail.com.
