On Wed, Apr 4, 2018 at 5:52 PM, Alexander Alexander <[email protected]> wrote: > Thanks Christoph. > > Finally my IBI (both bonded and nonbonded) is running know, but there is a > problem and that is the very high temperature (around 11842 K) which I get > by gmx energy over the ene.edr of each step while I use ref_t = 298.15 K in > my .mdp file using sd integrator. More or less I am using the grompp.mdp > file used in the tutorial examples. > Here is a part of it: > integrator = sd > tcoupl = no > tc-grps = System > tau_t = 1.0 > ref_t = 298.15 > Pcoupl = no > pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > gen_vel = yes > gen_temp = 298.15 > gen_seed = -1 > > I do not know what exactly is going on. Just a bunch on generic tips: Run longer, try a smaller timestep, watch the simulation in VMD to see if something looks strange.
> > > On Wednesday, April 4, 2018 at 9:04:27 AM UTC-4, Christoph Junghans wrote: >> >> On Tue, Apr 3, 2018 at 11:05 PM, Alexander Alexander >> <[email protected]> wrote: >> > Thank you Christoph. >> > >> > The gmx_mpi mdrun crashed in the step_001, with the below error; >> > >> > Tabulated interaction of type 'Tab. Bonds' or 'Tab. Bonds NC' with index >> > 0 >> > cannot be used because no table file whose name matched '_b0.xvg' was >> > passed >> > via the gmx mdrun -tableb command-line option. >> Yeah, there was a bug in gromacs-5.1 and since then you need to >> explicitly use "-tableb" in mdrun call. >> Usually VOTCA adds that automatically except if you have done it >> manually in settings xml file. >> It seems, you mis-numbered the tables in your topol.top: >> [ bonds ] >> 1 2 8 0 1 ; 1:bond-LG-H:1 >> 2 3 8 1 1 ; 1:bond-H-L:1 >> 3 4 8 1 1 ; 1:bond-L-RG:1 >> says you need a table_b0.xvg and table_b1.xvg (4th column is the table >> number - you using 0 and 1), but then you referring to table_b1.xvg, >> table_b2.xvg and table_b3.xvg in your settings.xml, so something is >> wrong here. >> >> (See the hexane/ibi_all for tutorial for details) > > I see now, I was not familiar with the [ bond ] (type 8) in tabulated > potential. >> >> >> > >> > But, it worked when I added "-tableb table_b0.xvg table_b1.xvg >> > table_b2.xvg >> > table_a0.xvg table_a1.xvg" to the gmx_mpi mdrun, I was surprised because >> > it >> > had thought the -tableb is kind of default when one intend to use >> > tabulated >> > potential calming in case.mdp file. (gromacs2018.1). >> As you aren't referring to table_b0.xvg anywhere in your settings.xml >> file, I am not sure where this table is coming from. >> >> > >> > More questions; >> > >> > Similar to the normal atomistic simulation, I was wondering if the >> > minimization and equalization are needed for IBI (bonded and nonbonded) >> > prior to the sd simulation in each step? >> VOTCA can do both, a minimization can be done before the main >> simulation (see the spce/simplex/simple example). >> For equalization, just set the <equi_time> in the xml file to >> something bigger than 0 and VOTCA will skip these parts of the >> simulation (similar to gmx's -b option) >> But if you need one of the two options is system dependent. >> >> > >> > By csg_map one can map the atomistic.trr to CG.xtc, what could be the >> > usage >> > of CG.txc in IBI (bonded and nonbonded) then? >> E.g. if you want to calculate some other properties of the CG system >> with gmx's tools, like diffusion constant. >> >> > >> > Should the conf.gro used in IBI be correspond to the conf.gro used in >> > the >> > all atom simulation? To be clear, if the CG.gro used in IBI must be >> > exactly >> > the one obtained by mapping the AA.gro and can not be bigger than that? >> > Can >> > we make the CG.gro obtained by mapping twice to use it in IBI? >> Actually it is very common to scale up the system for IBI to get more >> statistics. >> And you don't have to use exactly the same starting configuration, but >> you should use one which is equilibrated (which is the case for mapped >> ones.) >> > You mean we can generate a new bigger CG-conf.gro using for example gmx > insert-molecules, equilibrate it before any IBI. The equilibration should be > performed in CG level? If so, then who? because we still do not have any > good CG parameter for it to use them for equilibrating the scaled > CG-conf.gro. > Probably, we have to scale the system in atomistic level and equilibrate it > still in atomistic level and then mappe the scaled-equilibrated.gro to have > a CG-scaled-equilibrated.gro. You are right as the potential changes, "equilibrated" might have been the wrong word. I meant an initial condition without atoms overlaps like the mapped one. To build a bigger initial condition you can use e.g. "gmx genconf -nbox". Christoph > > Best regards, > Alex >> >> > >> > In using gmx rdf, we usually compare a selection (-sel) like A with a >> > reference (-ref) like B, and this means rdf_A_B.xvg might differ with >> > the >> > situation where we switch the reference and selection to have >> > rdf_B_A.xvg. >> > So, should we also consider this in for example csg_stat in setting,xml >> > or >> > map.xml? in other words, should we define both <nonbonded> A B >> > </nonbonded> >> > and <nonbonded> B A </nonbonded>? >> Honestly, there is only one interaction between A and B, so why would >> you calculate two RDFs? >> Also the way csg_stat calculates RDFs is symmetric. >> >> Christoph >> >> > >> > Thanks for your time in advance. >> > >> > Best regards, >> > Alex >> > >> > On Tuesday, April 3, 2018 at 5:29:00 AM UTC-4, Christoph Junghans wrote: >> >> >> >> >> >> >> >> On Tue, Apr 3, 2018, 09:31 Alexander Alexander <[email protected]> >> >> wrote: >> >>> >> >>> Dear all, >> >>> >> >>> I am iterating over the both bonded and nonbonded interactions in my >> >>> system using IBI. I also let program to guess all the initial >> >>> potential in >> >>> step_000. So, I do not need any external potential, but the program >> >>> crashes >> >>> in the step_001 requiring a table.xvg, I have attached my input files >> >>> in a >> >>> zip file, I would be so appreciated if you could have a look and help >> >>> me >> >>> overcome the problem. >> >> >> >> >> >> I was wrong, the table.xvg is still needed even with gromacs-2016. So >> >> just >> >> create a table.xvg with all zeros as y columns (or copy one over from >> >> one of >> >> tutorials) >> >> >> >> See the gromacs manual on details for the table format of table.xvg! >> >> >> >> Christoph >> >> >> >>> >> >>> >> >>> Thank you. >> >>> >> >>> Best regards, >> >>> Alex >> >>> >> >>> -- >> >>> 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 post to this group, send email to [email protected]. >> >>> Visit this group at https://groups.google.com/group/votca. >> >>> For more options, visit https://groups.google.com/d/optout. >> > >> > -- >> > 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 post to this group, send email to [email protected]. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
