Re: [votca] Relative entropy error in votca

On Tue, Apr 23, 2024 at 3:22 PM SAYAN DUTTA wrote: > > Here with I am attaching inverse.log and settings.xml file. Thanks, I understand the error, but it seems nobody has ever done relative entropy with pressure correction, hence it is not implemented. I think the way you could make that work is

Re: [votca] Relative entropy error in votca

Here with I am attaching inverse.log and settings.xml file. On Tue, Apr 23, 2024 at 11:55 PM Christoph Junghans wrote: > On Tue, Apr 23, 2024 at 2:52 PM SAYAN DUTTA > wrote: > > > > Here is the part of inverse.log which is throwing the error: > Send the full file, I want to look at the output

Re: [votca] Relative entropy error in votca

On Tue, Apr 23, 2024 at 2:52 PM SAYAN DUTTA wrote: > > Here is the part of inverse.log which is throwing the error: Send the full file, I want to look at the output to run_gromacs.sh as well above the error as well. Christoph > For all non-bonded > for_all: run 'do_external post_update_single

Re: [votca] Relative entropy error in votca

Here is the part of inverse.log which is throwing the error: For all non-bonded for_all: run 'do_external post_update_single re' for interaction named 'CG-CG' Running subscript 'post_update_re_single.sh' (from tags post_update_single re) dir

Re: [votca] Relative entropy error in votca

On Tue, Apr 23, 2024 at 11:58 AM SAYAN DUTTA wrote: > > Thank you Christoph, this seems to be working, but I am trying to apply > pressure correction with the potentials obtained from relative entropy. I > assume since works same like ibi, I added the pressure correction with > settings.xml

Re: [votca] Relative entropy error in votca

Thank you Christoph, this seems to be working, but I am trying to apply pressure correction with the potentials obtained from relative entropy. I assume since works same like ibi, I added the pressure correction with settings.xml file as follows : CG-CG.dist.tgt 1.0

Re: [votca] Relative entropy error in votca

On Mon, Apr 22, 2024 at 11:41 AM SAYAN DUTTA wrote: > > Hi Cristoph, I want to ask you this second question once again, because based > on the implementation of relative entropy it seems quite important to start > with initial_guess properly > I did this part as following way: > settings.xml

Re: [votca] Relative entropy error in votca

Hi Cristoph, I want to ask you this second question once again, because based on the implementation of relative entropy it seems quite important to start with initial_guess properly I did this part as following way: settings.xml file CG-CG CG CG 0 1.5 0.01 true

Re: [votca] Relative entropy error in votca

On Sat, Apr 20, 2024 at 6:10 PM SAYAN DUTTA wrote: > > Hi Christoph, Thank you so much for your reply, I tried to figure it out by > couple of possible ways, but failing for unknown reasons. Just trying to > understand a couple of viewpoints in terms of working with the relative > entropy

Re: [votca] Relative entropy error in votca

Hi Christoph, Thank you so much for your reply, I tried to figure it out by couple of possible ways, but failing for unknown reasons. Just trying to understand a couple of viewpoints in terms of working with the relative entropy based framework with votca-- 1. In the tutorial of spce/re with

Re: [votca] Relative entropy error in votca

On Thu, Apr 18, 2024 at 6:05 PM SAYAN DUTTA wrote: > > Hi, I am facing a trouble for running re, I am trying to use relative entropy > framework for liquid methanol (single site coarse grained model), I am > getting this error after 2nd iteration > table_average.sh: averaging with awk failed >

[votca] Relative entropy error in votca

Hi, I am facing a trouble for running re, I am trying to use relative entropy framework for liquid methanol (single site coarse grained model), I am getting this error after 2nd iteration table_average.sh: averaging with awk failed CG-simulation-with-REM/step_001/A-A.param.cur.9Dv5' x-value

Re: [votca] Relative entropy error

On Fri, Feb 21, 2020 at 2:26 AM Erez Tamir wrote: > > Dear all, > > I'm trying to apply the relative entropy (RE) method, with LJ 12-6 > interactions, for polymer melt containing 8 bead types. > My final goal is to reproduce mechanical properties of the atomistic system > by CG potentials. > In

[votca] Relative entropy error

Dear all, I'm trying to apply the relative entropy (RE) method, with LJ 12-6 interactions, for polymer melt containing 8 bead types. My final goal is to reproduce mechanical properties of the atomistic system by CG potentials. In order to obtain reasonable initial guess I used the IBI method

Re: [votca] relative entropy with lj126 interactions

Hi Tom, You can provide initial guess for LJ interaction parameters for relative entropy as #x y 0 1.0e-6 1 1.0e-3 where first y value corresponds to C12 and second y value corresponds to C6. Cheers, Sikandar On Fri, Sep 29, 2017 at 7:55 AM, Tom wrote: > > Hi, > > I

Re: [votca] Relative entropy - long range Coulomb pressure

Hi, As Christoph suggested, read in the file and store time series of energy values into an array (or table data type). First verify the accuracy of the implementation in a serial version of the code. The multi-threaded parallel version of relative entropy is handled for CsgREupdateWorker class.

Re: [votca] Relative entropy - long range Coulomb pressure

2017-01-30 8:00 GMT-05:00 Mohammad Motevaselian : > Hi, > > I am trying to implement long range Coulomb contribution to the pressure. I > do not want to calculate this in a direct way ( short range electrostatic + > PME), rather > I use Gromacs to give the Coulomb energy

[votca] Relative-Entropy

Hi, I was looking at the relative entropy code and find out the current version only linearly extrapolates the knot values less than rmin. Is there any reason not to extrapolate exponentially? And does it make a difference? Sincerely, Mohammad -- You received this message because you are

Re: [votca] Relative-Entropy

Hi Mohammad, The extrapolated potential for r rmin must be repulsive always, otherwise CG-MD simulations will crash. Both the linear and exponential extrapolations (given by following expressions) use the slope of the potential at rmin from relative entropy update. 'm = dy/dx - constant:

[votca] Relative Entropy

Dear all A few weeks ago I read something that relative entropy as a coarse grain method is implemented on Votca 1.3, this is the development version, is this correct ? There are any tutorial o paper on it ? Best Regards Marc Dr.Marc Segovia Universidad de la Republica Uruguay -- You

Re: [votca] Relative Entropy

Christoph, thanks for your answer and information.regards.marc On Thu, Oct 25, 2012 at 2:30 PM, Christoph Junghans jungh...@votca.org wrote: Hi, 2012/10/25 Marc Segovia marcsego...@gmail.com: Dear all A few weeks ago I read something that relative entropy as a coarse grain method is