Re: [votca] IBI is not able to reproduce the Target RDF for some interaction in the system

On Thu, Dec 22, 2022 at 1:11 PM Sanjeet Singh wrote: > > Hello Christoph, > > I am working on a Polymer-Water system and polymer is the bulk entity of my > system. > > I am trying to get the CG non-bonded potential for the Polymer-Water system > using IBI. I have 10 different types of

[votca] IBI is not able to reproduce the Target RDF for some interaction in the system

Hello Christoph, I am working on a Polymer-Water system and polymer is the bulk entity of my system. I am trying to get the CG non-bonded potential for the Polymer-Water system using IBI. I have 10 different types of interaction in my system. And IBI is not able to reproduce the RDF for the

Re: [votca] IBI of 500-mer polymer chain

On Thu, Feb 25, 2021 at 11:17 PM Pragati Sharma wrote: > > Thanks Christoph, I got a python script here in group chat and after > modifying it, I can easily make mapp.xml for 500 polymer. > > I am running NPT simulation of the polymer with the obtained tabulated > potentials. However I have a

Re: [votca] IBI of 500-mer polymer chain

Thanks Christoph, I got a python script here in group chat and after modifying it, I can easily make mapp.xml for 500 polymer. I am running NPT simulation of the polymer with the obtained tabulated potentials. However I have a few queries: 1. For obtaining potentials from IBI, NVT simulations

Re: [votca] IBI of 500-mer polymer chain

Pragati, you could use http://stock.cmm.ki.si/smt/, but for that size of a system you might need to write a little python script yourself. Christoph On Wed, Feb 24, 2021 at 3:36 AM Pragati Sharma wrote: > > Dear all, > > I am trying to perform IBI for a 500-mer polymer chain (Each monomer has

[votca] IBI of 500-mer polymer chain

Dear all, I am trying to perform IBI for a 500-mer polymer chain (Each monomer has 4 carbons and 6 Hs) I have tabulated potentials from IBI for a 10-mer and 32-mer chain containing 320 atoms and I will use these potentials to simulate the 500-mer polymer. However, a 500-mer polymer contains

Re: [votca] IBI of periodic molecules

On Thu, Feb 4, 2021 at 4:01 AM Pragati Sharma wrote: > > Hi Christoph, > > I tried increasing the box length in z direction, but the error still > persists. Its two layers of graphene each have 96 atoms. > > The errors is: > > "I have 192 beads in 2 molecules > I have 48 beads in 2 molecules for

Re: [votca] IBI of periodic molecules

Hi Christoph, I tried increasing the box length in z direction, but the error still persists. Its two layers of graphene each have 96 atoms. The errors is: "I have 192 beads in 2 molecules I have 48 beads in 2 molecules for the coarse graining Reading frame 0 time0.000

Re: [votca] IBI of periodic molecules

On Sat, Jan 16, 2021 at 1:40 AM Pragati Sharma wrote: > > Dear all, > > Can the coarse grain potentials using IBI for graphene sheet which is > periodic along xy direction be performed in votca. > > I am trying to do it and it's throwing an error saying the "bead is bigger > than half of the

[votca] IBI of periodic molecules

Dear all, Can the coarse grain potentials using IBI for graphene sheet which is periodic along xy direction be performed in votca. I am trying to do it and it's throwing an error saying the "bead is bigger than half of the box". Any ideas on this. Thanks -- Join us on Slack:

[votca] IBI non_bonded interaction convergence

Dear all, I performed an IBI iteration of non_bonded interaction on 400 hexane molecules using VOTCA and Lammps, After 1000 steps of iteration, there is still no convergence. I have tried to modify parameters such as cutoff, table_bins, scaling, etc.. The following is a comparison of the

[votca] IBI non_bonded interaction Iteration convergence

Dear all, I performed an IBI iteration of non_bonded interaction on 400 hexane molecules using VOTCA and Lammps, After 1000 steps of iteration, there is still no convergence. I have tried to modify parameters such as cutoff, table_bins, scaling, etc.. The following is a comparison of the

Re: [votca] IBI error: segmentation fault at csg_inverse step of IBI in step001

On Wed, Aug 5, 2020 at 5:45 AM 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

Re: [votca] Ibi tutorial with lammps

On Tue, May 26, 2020 at 12:59 PM sandip khan wrote: > > Dear All, > > I was running the ibi tutorial with lammps for spce water model. I > got following error in the inverse.log file for step001. However lammps > simulation done in folder "step-001" > What version of VOTCA are you

[votca] Ibi tutorial with lammps

Dear All, I was running the ibi tutorial with lammps for spce water model. I got following error in the inverse.log file for step001. However lammps simulation done in folder "step-001" Topology does not have beads of type "Bead1" This was specified in type1 of interaction "CG-CG"

Re: [votca] IBI on a polymer melt

On Thu, Jan 16, 2020 at 8:38 AM CHRISTINA-ANNA GATSIOU < christianna.gats...@gmail.com> 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. >

Re: [votca] IBI on a polymer melt

On Wed, Jan 8, 2020 at 02:56 CHRISTINA-ANNA GATSIOU < christianna.gats...@gmail.com> 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

Re: [votca] IBI on a polymer melt

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

Re: [votca] IBI on a polymer melt

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 > > 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

Re: [votca] IBI on a polymer melt

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 < > christian...@gmail.com > wrote: > >> Hi Christoph, >> >> I have set all exclusions in the gromacs topology file. However, during >> IBI for one nonbonded

Re: [votca] IBI on a polymer melt

On Fri, Jan 3, 2020 at 8:13 AM CHRISTINA-ANNA GATSIOU < christianna.gats...@gmail.com> 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

Re: [votca] IBI on a polymer melt

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

Re: [votca] IBI on a polymer melt

On Sat, Dec 14, 2019 at 11:27 CHRISTINA-ANNA GATSIOU < christianna.gats...@gmail.com> 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

Re: [votca] IBI on a polymer melt

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 ? Thanks for the prompt response. Best regards, Christianna > On 14 Dec 2019, at 1:26

Re: [votca] IBI on a polymer melt

On Fri, Dec 13, 2019 at 3:35 PM CHRISTINA-ANNA GATSIOU wrote: > > Dear Christoph, > > I am working on a polymer melt and I am consistently getting rdfs for > nonbonded interactions that look like the attachment. I get a peak where > there is a bond and it shouldn't be counted as a non bonded

[votca] IBI on a polymer melt

Dear Christoph, I am working on a polymer melt and I am consistently getting rdfs for nonbonded interactions that look like the attachment. I get a peak where there is a bond and it shouldn't be counted as a non bonded interaction. I saw in earlier posts that one should first derive the

Re: [votca] IBI for crystalline phase

On Mon, Dec 2, 2019 at 2:36 AM Souvik Chakraborty wrote: > > Dear Christoph, > > I am trying to implement IBI for a crystalline phase coarse-grained from an > equillibrated united-atom model. So, the target rdf has a long-range order > (attached). > > Before doing IBI step, I am trying to

Re: [votca] IBI on polymer chains mixture

Erez, On Sun, Sep 22, 2019 at 10:33 AM Christoph Junghans wrote: > > On Sun, Sep 22, 2019 at 8:41 AM Erez Tamir wrote: > > > > Is this mean I currently can't use version 1.5 with my pdb files? > Correct. Hopefully we will get around to fixing it soon. Can you test this fix:

Re: [votca] IBI on polymer chains mixture

On Sun, Sep 22, 2019 at 8:41 AM Erez Tamir wrote: > > Is this mean I currently can't use version 1.5 with my pdb files? Correct. Hopefully we will get around to fixing it soon. > Is there option for workaround or disabling the rigorous pdb reader in this > version? Unfortunately not. > > Is

Re: [votca] IBI on polymer chains mixture

Is this mean I currently can't use version 1.5 with my pdb files? Is there option for workaround or disabling the rigorous pdb reader in this version? Is there former version supporting pressure correction for lammps and relative entropy which are important to my research? What do you suggest?

Re: [votca] IBI on polymer chains mixture

On Sun, Sep 22, 2019 at 7:48 AM Erez Tamir wrote: > > Hi Christoph, > Thank you for answering, your support is invaluable. > > I see you get a different error message for the csg_dump command. > I still get the error: > > an error occurred: > map::at > > Why is this difference? I've installed

Re: [votca] IBI on polymer chains mixture

Hi Christoph, Thank you for answering, your support is invaluable. I see you get a different error message for the csg_dump command. I still get the error: an error occurred: map::at Why is this difference? I've installed the latest stable votca version.. I've also tried to find the code file

Re: [votca] IBI on polymer chains mixture

On Sun, Sep 22, 2019 at 3:38 AM Erez Tamir wrote: > > I made some modifications in the pdb file in order to stick to the pdb > specifications and now the following message appears: > > an error occurred: > map::at > > What this error means? > Is this means that votca now can read my pdb file but

Re: [votca] IBI on polymer chains mixture

On Fri, Sep 20, 2019 at 6:21 AM Erez Tamir wrote: > > Hi, > I overcome the previous issue, and now facing another problem: > After installing the latest stable release v1.5 I have problem reading pdb > files that worked fine with older version. > When performing csg_dump or cag_stat for example

Re: [votca] IBI on polymer chains mixture

On Wed, Aug 21, 2019 at 1:48 AM Erez Tamir wrote: > > Dear all, > > I'm trying to perform IBI on polymer system contains 20 different molecules > (each molecule is a polymer chain). > The molecules differ by their structure, but they share the same bond and > angle types. I don't think that is

Re: [votca] IBI bonded potentials

On Sun, May 12, 2019 at 12:53 PM CHRISTINA-ANNA GATSIOU wrote: > > Hi, > > I have been trying to perform IBI on a PEG oligomer (6 monomers). I have used > only one bead type for each monomer. This degrees of freedom of my cg system > are one bond type , one angle type, one dihedral type and one

[votca] IBI bonded potentials

Hi, I have been trying to perform IBI on a PEG oligomer (6 monomers). I have used only one bead type for each monomer. This degrees of freedom of my cg system are one bond type , one angle type, one dihedral type and one nonbonded interaction. I have generated a sufficiently long trajectory

Re: [votca] IBI on a binary mixture

On Thu, May 9, 2019 at 6:24 AM CHRISTINA-ANNA GATSIOU wrote: > > Hi, I would like to ask a slightly different question. In case I want to run > a parallel lammps job. What would be the entry in settings.xml? > I tried > lammps > > mpirun lammps Run "mpirun -nt 4 lammps" here and drop

Re: [votca] IBI on a binary mixture

Hi, I would like to ask a slightly different question. In case I want to run a parallel lammps job. What would be the entry in settings.xml? I tried lammps mpirun lammps -nt 4 But it does not seem to work. I get the error message that the command is not found. > On 8 May 2019,

Re: [votca] IBI on a binary mixture

On Wed, May 8, 2019 at 10:40 AM CHRISTINA-ANNA GATSIOU wrote: > > Hi, > I would like to ask one additional question. So the csg_stat during IBI is > calculated by the following scripts: > 1)calc_rdf_generic.sh > 2)calc_target_rdf_generic.sh > > I guess the second one is not used during

Re: [votca] IBI on a binary mixture

Hi, I would like to ask one additional question. So the csg_stat during IBI is calculated by the following scripts: 1)calc_rdf_generic.sh 2)calc_target_rdf_generic.sh I guess the second one is not used during inversion. Are there any additional scripts used. Christianna > On 8 May 2019,

Re: [votca] IBI on a binary mixture

On Wed, May 8, 2019 at 8:22 AM CHRISTINA-ANNA GATSIOU wrote: > > Yes I understand this but I what I do not understand why or where it fails to > generate this. It should be generated by csg_stat. Just look for the last csg_stat execution in the log file before the error occurs. Christoph > > --

Re: [votca] IBI on a binary mixture

On Wed, May 8, 2019, 01:43 CHRISTINA-ANNA GATSIOU < christianna.gats...@gmail.com> wrote: > Hi, > > Thanks for the help! The error message I get now looks like this: > Running subscript 'update_ibi_pot.pl P4_P4.dist.tgt P4_P4.dist.new > P4_P4.pot.cur P4_P4.dpot.pure_ibi' (from tags update

Re: [votca] IBI on a binary mixture

Hi, Thanks for the help! The error message I get now looks like this: Running subscript 'update_ibi_pot.pl P4_P4.dist.tgt P4_P4.dist.new P4_P4.pot.cur P4_P4.dpot.pure_ibi' (from tags update ibi_pot) dir /usr/s hare/votca/scripts/inverse readin_table: could not open file P4_P4.dist.new

Re: [votca] IBI on a binary mixture

I found it, it was actually a bug in the code, when using multiple mapping files, which I fixed here: https://github.com/votca/csg/pull/371 As a workaround apply the patch or revert the order of the mapping files in your settings.xml for now: --- settings.xml.orig 2019-04-27 19:42:45.434237893

Re: [votca] IBI on a binary mixture

The error message looks like this for_all: run 'do_external prepare_single ibi' for interaction named 'P2-P1' Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /scratch/cgatsiou/votca/share/votca/scripts/inverse Callstack:

Re: [votca] IBI on a binary mixture

On Fri, Apr 26, 2019, 07:52 wrote: > Hi, > > > I have attached the neccessary files. IBI seems to be failing before the > inversion of the initial distributions! Some help would be very much > appreciated. > What is the error message? Christoph > > > Best regards, > Christianna > > -- > You

[votca] IBI for Lipid + Ethanol

Dear friends, MARTINI FF shows aggregation of lipids in ethanol which is not realistic, so I am trying to develop CG-force filed for a system of DPPC in Ethanol solvent (all-atom simulation as a reference carried out with CHARMM36 at P=1bar, T=330K). DPPC is mapped to a CG similar to MARTINI

Re: [votca] IBI non bonded interaction for DGEBA

On Tue, Dec 18, 2018 at 8:44 PM Lee wrote: > >I have fitted the distribution by Gaussian curve (the red line) and > use it as the target distribution. But the converted potential presents not a > harmonic form (as shown in ACF.pot.cur.png). I want to know what causes the > potential

Re: [votca] IBI non bonded interaction for DGEBA

I have fitted the distribution by Gaussian curve (the red line) and use it as the target distribution. But the converted potential presents not a harmonic form (as shown in ACF.pot.cur.png). I want to know what causes the potential curve drops sharply at the boundary PI. And I

Re: [votca] IBI non bonded interaction for DGEBA

On Tue, Dec 18, 2018 at 6:14 AM Lee wrote: > > Hi Christoph, >Now I want to fit the target distribution with single peak gaussian > distribution. So the angle potential can be expressed with harmonic potential > (quadratic form). But if the peak of angle distribution close to PI, the >

Re: [votca] IBI non bonded interaction for DGEBA

On Fri, Dec 7, 2018 at 4:54 AM Lee wrote: > > After I added the pressure correction, the density of the cg system is very > close to the full-atomic system. Thanks for your advise. But when I use these > final potential table to do the tensile simulation for cg system, the system > is

Re: [votca] IBI non bonded interaction for DGEBA

After I added the pressure correction, the density of the cg system is very close to the full-atomic system. Thanks for your advise. But when I use these final potential table to do the tensile simulation for cg system, the system is unstable. And the stress-strain curve is extrmely terrible. I

Re: [votca] IBI non bonded interaction for DGEBA

On Mon, Dec 3, 2018 at 3:51 AM Lee wrote: > >Yes, you are right. I missed a important item, pressure correction. > But when I add pressure into the , the error occurred "Pressure > correction for lammps is not implemented yet". Does the pressure correction > need to be implemented

Re: [votca] IBI non bonded interaction for DGEBA

Yes, you are right. I missed a important item, pressure correction. But when I add pressure into the , the error occurred "Pressure correction for lammps is not implemented yet". Does the pressure correction need to be implemented additionally? And how to implement it? Thanks 在

Re: [votca] IBI non bonded interaction for DGEBA

On Sun, Dec 2, 2018 at 6:40 PM Lee wrote: > > By checking the convergence value of interaction, I found that it was > stabilized above 1. When I use these potential table to do the cg simulation, > the density of cg system is half of that the corresponding atomic system. So > I think the

Re: [votca] IBI non bonded interaction for DGEBA

On Fri, Nov 30, 2018 at 8:00 PM Lee wrote: > > OK, thanks! I have increased the bin size and the distribution seems to > be smoothed. > In some paper, the IBI process is started from bond and then angle, the > nonbonded potential is finished at last. When doing ibi for bond and

Re: [votca] IBI non bonded interaction for DGEBA

I have a problem in installation when I'm going to install it at another computer. When I run the csg_inverse command and the ERROR "source_wrapper: Could not get any script from tags 'functions' 'lammps' " occurs. I'm sure that I have installed lammps in this computer. So what's the proplem?

Re: [votca] IBI non bonded interaction for DGEBA

OK, thanks! I have increased the bin size and the distribution seems to be smoothed. In some paper, the IBI process is started from bond and then angle, the nonbonded potential is finished at last. When doing ibi for bond and angle, the pair interaction is turned off. The chains

Re: [votca] IBI non bonded interaction for DGEBA

On Fri, Nov 30, 2018 at 01:05 Lee wrote: > In votca, the smoothing process works for potential. Is there any > smoothing process for new distribution? And what's the command? > No, but it would be hard to add! Also increasing the bin size naturally does smoothing! Christoph > > > 在

Re: [votca] IBI non bonded interaction for DGEBA

In votca, the smoothing process works for potential. Is there any smoothing process for new distribution? And what's the command? 在 2018年11月21日星期三 UTC+8下午9:03:19，Christoph Junghans写道： > > On Tue, Nov 20, 2018 at 6:44 PM Lee > > wrote: > > > > The expression of boltzmann inversion is

Re: [votca] IBI non bonded interaction convergence

On Wed, Nov 28, 2018 at 7:27 PM changseo park wrote: > > I did IBI for non bond interaction on PNIPAM chain in water. > > I got some reasonable and converged results from iteration. > > There two candidates for convergence > > the red peak shows the rdf from atomistic simulation, and the green

Re: [votca] IBI non bonded interaction for DGEBA

On Tue, Nov 20, 2018 at 6:44 PM Lee wrote: > > The expression of boltzmann inversion is V=-kBTln(P). And the distribution P > is related to the scale of the x-coordinate. The plot of bond distribution > with different units are attached. In votca, all the processes including > calculating

Re: [votca] IBI non bonded interaction for DGEBA

The expression of boltzmann inversion is V=-kBTln(P). And the distribution P is related to the scale of the x-coordinate. The plot of bond distribution with different units are attached. In votca, all the processes including calculating distributions and boltzmann inversion are finished with

Re: [votca] IBI non bonded interaction for DGEBA

On Tue, Nov 20, 2018 at 2:04 AM Lee wrote: > > I have another question. If my units command is real in lammps which the > units of distance and energy are angstroms and Kcal/mole respectively, what > shoud I change in the setting file in order to get the potential table with > right units?

Re: [votca] IBI non bonded interaction for DGEBA

I have another question. If my units command is real in lammps which the units of distance and energy are angstroms and Kcal/mole respectively, what shoud I change in the setting file in order to get the potential table with right units? Now, the bond and angle potential of the CG system

Re: [votca] IBI non bonded interaction for DGEBA

On Mon, Nov 19, 2018 at 8:51 AM Christoph Junghans wrote: > > On Sun, Nov 18, 2018 at 8:31 PM Lee wrote: > > > > For the dynamic simulations finished with lammps, should I set the > > exclusions? If excluding non-bonded interactions between atoms that are no > > further than 3 bonds away, does

Re: [votca] IBI non bonded interaction for DGEBA

On Sun, Nov 18, 2018 at 8:31 PM Lee wrote: > > For the dynamic simulations finished with lammps, should I set the > exclusions? If excluding non-bonded interactions between atoms that are no > further than 3 bonds away, does it need to excluding these atoms when > statistical target rdf

Re: [votca] IBI non bonded interaction for DGEBA

For the dynamic simulations finished with lammps, should I set the exclusions? If excluding non-bonded interactions between atoms that are no further than 3 bonds away, does it need to excluding these atoms when statistical target rdf distributon? -- You received this message because you are

Re: [votca] IBI non bonded interaction for DGEBA

On Sat, Nov 17, 2018 at 7:38 PM Lee wrote: > > The lammps dump files are attached. What's the meaning of layering as you > said? I was referring to the RDFs, which have some big zickzack pattern in there. Christoph > > 在 2018年11月17日星期六 UTC+8下午9:15:00，Christoph Junghans写道： >> >> On Fri, Nov 16,

Re: [votca] IBI non bonded interaction for DGEBA

On Fri, Nov 16, 2018 at 6:30 PM Lee wrote: > > Thanks for your reply. The attached files are the new rdf of the last > iteration step with target rdf distributions. Is the trend correct? Does it > converge if the iteration isn't interrupted? And do you have any suggestions > of my setting

Re: [votca] IBI non bonded interaction convergence

On Wed, Oct 17, 2018 at 7:18 AM changseo park wrote: > > I already contact with the author you mentioned. Thanks. > > For checking the dependency of non-bonded potential each other for any system, > > If I changed the AA potential and the other non bonded rdf is consistent, is > it enough to say

Re: [votca] IBI non bonded interaction convergence

I already contact with the author you mentioned. Thanks. For checking the dependency of non-bonded potential each other for any system, If I changed the AA potential and the other non bonded rdf is consistent, is it enough to say AA potential is independent to other potential? or still AA non

Re: [votca] IBI non bonded interaction convergence

On Wed, Oct 17, 2018 at 6:41 AM changseo park wrote: > > OK, the more RDF and averaging them will not help. > > About my system, PNIPAM in water, I'm working on CG parameterization for 280K > state which is Coil state based on All atom results( LOPLS + TIP4P/2005) > > I confirmed that the all

Re: [votca] IBI non bonded interaction convergence

OK, the more RDF and averaging them will not help. About my system, PNIPAM in water, I'm working on CG parameterization for 280K state which is Coil state based on All atom results( LOPLS + TIP4P/2005) I confirmed that the all atom scale PNIPAM has extended structure at 280K and collapsed

Re: [votca] IBI non bonded interaction convergence

On Tue, Oct 16, 2018 at 12:57 AM changseo park wrote: > > After getting sum advice and searching several queries, I did IBI for > non-bonded, but still I couldn't get the converged non bonded potential > > My system composed of one 30m PNIPAM chain in dilute water. the polymer chain > composed

Re: [votca] IBI non bonded interaction convergence

On Fri, Oct 5, 2018 at 7:11 AM changseo park wrote: > > > Thanks for quick answer!! > > Okay, the main criteria for convergence is to compare the distribution > function one by one with target function > > In my case, the Convergence sum is start from 15000 and after step 2, it > varies from

Re: [votca] IBI non bonded interaction convergence

Thanks for quick answer!! Okay, the main criteria for convergence is to compare the distribution function one by one with target function In my case, the Convergence sum is start from 15000 and after step 2, it varies from 3000~5000 in every step until more than 300 step when I compared the

Re: [votca] IBI non bonded interaction convergence

On Fri, Oct 5, 2018 at 6:12 AM changseo park wrote: > > TO. VOTCA users > > Hi, I'm new user for VOTCA. > > I'm researching about one single chain polymer conformation change in water > dilute system. > > I figured out all the errors based on queries on VOTCA and I started the IBI > step. > >

Re: [votca] ibi-all after ibi-nonbonded

On Tue, Apr 24, 2018 at 3:37 AM, Alexander Alexander wrote: > Dear all, > > After successfully doing IBI over nonbonded parameter of my system cantoning > 3 beads-3 type, I am doing IBI on both bonded and nonbonded together. The > system has 2 bonds and one angle. As

[votca] ibi-all after ibi-nonbonded

Dear all, After successfully doing IBI over nonbonded parameter of my system cantoning 3 beads-3 type, I am doing IBI on both bonded and nonbonded together. The system has 2 bonds and one angle. As the attached figure shows all of the bonded parameters (two bonds and one angle) getting worse

Re: [votca] IBI convergence

2017-02-21 0:11 GMT-07:00 Arpita : > Dear VOTCA users, > I am using IBI method to get the correct parameters of non-bonded potentials > for CG simulations using the AA distributions as the target RDF. I have many > non-bonded interactions in my surfactant-water system but first I

[votca] IBI convergence

Dear VOTCA users, I am using IBI method to get the correct parameters of non-bonded potentials for CG simulations using the AA distributions as the target RDF. I have many non-bonded interactions in my surfactant-water system but first I am trying to get the correct distribution for the

[votca] IBI

Dear VOTCA users, I am coarse graining a surfactant molecule. I am deriving the bonded potentials using IBI. First I got the distributions of bonds and angles due to mapping of atomistic model to a coarse-grained model, and from those distributions, bonded potentials were derived. Then those

Re: [votca] IBI

Dear Arpita, first of all, please don't reply to a mail thread related to a different issue that make it really hard to search on the mailing list later, just start a new one. Second, I assume, you have solved your original issue, so please post your solution, so that others can learn from it.

[votca] IBI - correlation between number of beads and convergence

Dear Votca Users, I have 6 bead types, thus have 21 non-bonded interaction. When I try other tutorials (mostly 2 bead types) from csg_tutorials, it seems that convergence reaches within few steps. In my case of 6 bead types, more than 6 interactions still have not been converged even over 100

Re: [votca] IBI run- few of RDF does not converge

2016-08-15 12:49 GMT-06:00 Chang Woon Jang : > Dear Christoph, > >I have iterated the interactions only not converged RDFs from step_300. > Now, it reaches step_400. The new RDFs do not seem to converge the target > RDFs. > > Is this because of so many non-bonded

Re: [votca] IBI run- few of RDF does not converge

2016-08-08 14:24 GMT-06:00 Chang Woon Jang : > Dear Christoph, > > I have followed the option 1) Stop after 300 steps, change your > settings.xml (i.e. set do_potential to "0" for converged potentials) and go > on in the same directory structure.) > > When I set

Re: [votca] IBI run- few of RDF does not converge

Dear Christoph, I have followed the option 1) Stop after 300 steps, change your settings.xml (i.e. set do_potential to "0" for converged potentials) and go on in the same directory structure.) When I set do_potential to "0" for few of interactions, for example A-B, the radial distributions

Re: [votca] IBI run- few of RDF does not converge

2016-08-08 10:26 GMT-06:00 Chang Woon Jang : > Dear Christoph, > > Thank you for your comments. If I iterate only not converged potentials, > can I use the potentials converged over 300 steps? Yes! > > >Do I need to just modify the settings.xml file to iterate

Re: [votca] IBI run- few of RDF does not converge

Dear Christoph, Thank you for your comments. If I iterate only not converged potentials, can I use the potentials converged over 300 steps? Do I need to just modify the settings.xml file to iterate only not converged RDFs? Do I just remove all converged RDFs, ? Thank you very much.

[votca] IBI run- few of RDF does not converge

Dear Votca Users, I have run IBI for the system with 7 types of beads. Total 28 non-bonded interactions. I have reached 500 steps. Each step runs about 8 ns (800 iterations). Few of RDFs do not converge to the target RDFs. I keep running the IBI but the RDFs do not seem to be converged

Re: [votca] IBI for bonded interactions

2016-05-24 11:43 GMT-06:00 Takahiro Ohkuma : > Yes. No jumps now appear in the distribution by setting proper values of > min, max, and step. Cool, so I merged my earlier fix! Christoph > > Thanks, > Takahiro > > 2016年5月24日火曜日 14時19分02秒 UTC+2 Christoph Junghans: >> >> >>

Re: [votca] IBI for bonded interactions

Yes. No jumps now appear in the distribution by setting proper values of min, max, and step. Thanks, Takahiro 2016年5月24日火曜日 14時19分02秒 UTC+2 Christoph Junghans: > > > Am 24.05.2016 06:15 schrieb "Takahiro Ohkuma" >: > > > > Dear Christoph > > > > Thank you for the update.

Re: [votca] IBI for bonded interactions

Am 24.05.2016 06:15 schrieb "Takahiro Ohkuma" : > > Dear Christoph > > Thank you for the update. It is fine. Does it fix the issue of the jumping distribution? Christoph > > Takahiro > > > 2016年5月23日月曜日 21時14分37秒 UTC+2 Christoph Junghans: >> >> 2016-05-23 5:23 GMT-06:00

Re: [votca] IBI for bonded interactions

Dear Christoph Thank you for the update. It is fine. Takahiro 2016年5月23日月曜日 21時14分37秒 UTC+2 Christoph Junghans: > > 2016-05-23 5:23 GMT-06:00 Takahiro Ohkuma >: > > Dear Christoph > > > > I found a possible way to avoid the jumps in dihedral distributions. > > There

Re: [votca] IBI for bonded interactions

2016-05-23 5:23 GMT-06:00 Takahiro Ohkuma : > Dear Christoph > > I found a possible way to avoid the jumps in dihedral distributions. > There are 3 points I should notice. > > (1) > The bin range of the histogram is made as [ x - 0.5 * step , x + 0.5 * > step]. > Therefore,

Re: [votca] IBI for bonded interactions

Dear Christoph I found a possible way to avoid the jumps in dihedral distributions. There are 3 points I should notice. (1) The bin range of the histogram is made as [ x - 0.5 * step , x + 0.5 * step]. Therefore, when I choose min=-3.14, max=3.14, and step=0.04, the histogram gets sudden drops

Re: [votca] IBI for bonded interactions

2016-05-19 11:07 GMT-06:00 Takahiro Ohkuma : > Dear Christoph > > I am really grateful for writing a patch. > Unfortunately, the patch seems not to help for my problem. > I obtained almost the same results for the dihedral distribution and the > inverted potential. They

Re: [votca] IBI for bonded interactions

Dear Christoph I am really grateful for writing a patch. Unfortunately, the patch seems not to help for my problem. I obtained almost the same results for the dihedral distribution and the inverted potential. They still have jumps at the data ends. Just to make sure, I would like to write down

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