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. 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] <javascript:>> 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. 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
