Dear Christoph, On Thursday, April 5, 2018 at 6:46:13 AM UTC-4, Christoph Junghans wrote: > > On Wed, Apr 4, 2018 at 5:52 PM, Alexander Alexander > <alexand...@gmail.com <javascript:>> 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. >
The temperature is now fine around 298.15 k, to reach that although I had to use dt = 0.00002 but the key point was tau_t which I changed it to 0.02 from 1.0 to have the temperature correct finally. But the pressure is too high around 1143.92 in each step, which I found it that is normal when I compared with your spce-ibi example which has 6000 or 8000 of pressure in each step, am I right, please? One more issue: In my IBI (bonded and nonbonded), I get errors like ""inverse/dist_boltzmann_invert.pl --type dihedral --kbT 2.4789711565 --min 1e-10 bond-LA-LB.dist.tgt bond-LA-LB.pot.new.raw.NK3 " for the bonds and angles. I can solve it by decreasing the step to <step>0.00001</step> for them, which then slows down everything and also the improvement in potentials and ... . What could be the reason for such an error? Thank you. Best regards, Alex > > > > > > > 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 > >> <alexand...@gmail.com> 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 <alexand...@gmail.com> > > >> >> 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 votca+un...@googlegroups.com. > >> >>> To post to this group, send email to vo...@googlegroups.com. > >> >>> 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 votca+un...@googlegroups.com. > >> > To post to this group, send email to vo...@googlegroups.com. > >> > 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 votca+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <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. 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