On Thu, Jan 16, 2020 at 8:38 AM CHRISTINA-ANNA GATSIOU < [email protected]> wrote:
> Hi Christoph, > > I managed to resolve the issue with non-bonded interactions by not using > the toopology.xml when fitting the non-bonded interactions and by using > nrexcl is 3 in topol.top. > However it does not make sense why it did not work before since bonds etc > were appropriately specified. > I looked at topology_.xml brief and it is really long, so I have two guesses: - you simply forgot to list a bond - nrexcl corresponds to 3 bond length exclusions, .i.e. in a bond A-B-C-D, A and D are excluded, even though there is no bond between A and D, so you would need to add a non-physical bond to your topology_.xml > There is one additional problem with the convergence of angles and > dihedrals. Having fixed the nonbonded interactions, the angle distributions > do not seem to improve. > dihedrals have long convergence in general, but angles could be slow as well depending on your system. Did you look at the angle auto-correlation time to get a feel if the distribution are sampled went enough? Christoph > > Best regards, > Christianna > > On Wednesday, January 8, 2020 at 3:10:37 PM UTC+2, Christoph Junghans > wrote: >> >> >> >> On Wed, Jan 8, 2020 at 02:56 CHRISTINA-ANNA GATSIOU < >> [email protected]> wrote: >> >>> Hi Christoph, >>> >>> "Ok, if you are using a mapping file (--cg option), the exclusion from >>> the tpr get mapped out." >>> Does this mean that I should not be using the mapping file in order for >>> the exclusions to be taken into account. I was under the impression that it >>> was necessary. I have already defined those bonds in the mapping file. >>> >> It depends, a mapping file is usually only needed if you want to do IBI >> on the bonded interactions as well. >> >> As VOTCA has no concept of nrexcl in gromacs once you map, you might need >> to more unphysical bonds, e.g. using a tpr with a chain with bonds A-B-C, A >> & C would be excluded if nrexcl is 2, after mapping A & B as well as B & C >> are excluded, but A & C are not, so you will need to add an unphysical bond >> between A & C to achieve that. Looking at the output of “csg_dump —excl >> —top topol” vs. “csg_dump —excl —top topol.tpr —cg map.xml” should reveal >> that. >> >> Can you send your tpr and mapping files? >> >>> >>> >>> >>> On Monday, January 6, 2020 at 8:34:01 PM UTC+2, Christoph Junghans wrote: >>> >>>> On Mon, Jan 6, 2020 at 10:26 AM CHRISTINA-ANNA GATSIOU >>>> <[email protected]> wrote: >>>> > >>>> > >>>> > >>>> > On Friday, January 3, 2020 at 5:30:28 PM UTC+2, Christoph Junghans >>>> wrote: >>>> >> >>>> >> >>>> >> >>>> >> On Fri, Jan 3, 2020 at 8:13 AM CHRISTINA-ANNA GATSIOU < >>>> [email protected]> wrote: >>>> >>> >>>> >>> Hi Christoph, >>>> >>> >>>> >>> I have set all exclusions in the gromacs topology file. However, >>>> during IBI for one nonbonded interaction I get the attached distribution >>>> (red corresponds to the bond distribution the bonded beads, green >>>> corresponds to the target distribution of bead types and blue to IBI >>>> distribution at step 30). It seems that bonded pairs are included in the >>>> g(r) even though I have specified them as non interacting in the exclusion >>>> list. I cannot figure out what might be the problem here. Thanks in >>>> advance. >>>> >> >>>> >> Go in the log file (usually inverse.log) and find the last csg_stat >>>> call (e.g. with "grep csg_stat inverse.log") and post it here. >>>> >> >>>> > csg_stat --nt 8 --options settings_nb.xml --top topol.tpr --trj >>>> traj.xtc --begin 5 --first-frame 0 --cg topology.xml; >>>> Ok, if you are using a mapping file (--cg option), the exclusion from >>>> the tpr get mapped out. You will need to add bonds between the atoms >>>> you want to exclude in mapping file. See here for an example: >>>> >>>> https://github.com/votca/csg-tutorials/blob/master/hexane/ibi_all/hexane_cg.xml#L25-L39 >>>> You don't need to do anything with these bonds in the IBI iterations. >>>> >>>> Again you can check the exclusions after mapping with csg_dump, e.g. >>>> $ csg_dump --excl --top topol.tpr --cg topology.xml >>>> >>>> Christoph >>>> > >>>> > >>>> >> >>>> >> Christoph >>>> >>> >>>> >>> >>>> >>> >>>> >>> Best regards, >>>> >>> Christianna >>>> >>> >>>> >>> On Saturday, December 14, 2019 at 8:52:34 PM UTC+2, Christoph >>>> Junghans wrote: >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Sat, Dec 14, 2019 at 11:27 CHRISTINA-ANNA GATSIOU < >>>> [email protected]> wrote: >>>> >>>>> >>>> >>>>> Hi Christoph, >>>> >>>>> >>>> >>>>> My topology.xml does contain exclusions. I have only specified >>>> nrexcl 3 which I thought should do the job. Do I need to specify exclusions >>>> in the topology.xml or in the gromacs topology file ? >>>> >>>> >>>> >>>> If you are using a tpr file as topology VOTCA will read the >>>> exclusions from there. If you are using a xml topology exclusions will be >>>> generated out of the bonds and angles. >>>> >>>> >>>> >>>> Just look in inverse.log what topology file is used by csg_stat >>>> and run csg_dump on it to check the exclusions. >>>> >>>> >>>> >>>> Christoph >>>> >>>>> >>>> >>>>> Thanks for the prompt response. >>>> >>>>> >>>> >>>>> Best regards, >>>> >>>>> Christianna >>>> >>>>> >>>> >>>>> On 14 Dec 2019, at 1:26 AM, Christoph Junghans <[email protected]> >>>> wrote: >>>> >>>>> >>>> >>>>> csg_dump --excl --top <topology_file> >>>> >>>>> >>>> >>>>> >>>> >>>>> -- >>>> >>>>> 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/7889732D-B264-4FBB-A951-271C1190FB7F%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/c927b5cc-550d-4388-b10f-ae598ec15753%40googlegroups.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/92a68fed-7eca-41d6-90cb-f7825f229c82%40googlegroups.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/c352c13c-4676-4b79-a75b-ddaa44ab9919%40googlegroups.com >>> <https://groups.google.com/d/msgid/votca/c352c13c-4676-4b79-a75b-ddaa44ab9919%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> 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/dba049a5-ec66-49d0-9a7b-122b13fc9dbc%40googlegroups.com > <https://groups.google.com/d/msgid/votca/dba049a5-ec66-49d0-9a7b-122b13fc9dbc%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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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