Re: [votca] Tabulated vs harmonic potential for a bond

Hi Alexander, In the very first e-mail, you have shown us the plot of table_.xvg, I suppose this is the forces column. Now you can see that the force is 0 before and after the region of interest. In fact, it does not matter how big K you put in topol.top for bond type 8, K*0 = 0. I think that's

Re: [votca] Re: Bonds in XML topology for LAMMPS trajectory

Dear Gustavo, (...) > Your reply made me realize that problem with the tab characters. Maybe > the XML > parser is getting confused with a mix of tabs and white spaces? > > In any case, now it works correctly (as long as only spaces are used). and > I > see the proper exclusions when I run

[votca] Re: Bonds in XML topology for LAMMPS trajectory

Dear Gustav, W dniu czwartek, 27 października 2016 15:16:58 UTC+2 użytkownik Gustavo Rondina napisał: > > Hello VOTCA folks, > > Since LAMMPS dump files provide no topological information, I'm doing as > instructed in the manual and using a XML topology. However, I'm not quite > sure how to

Re: [votca] mapping lammps trajectory

2016-07-14 3:52 GMT+02:00 Sikandar Mashayak : > Hi, > > I am testing a case in which I want to compute water-water RDF from the > lammps trajectory. > > So, I need to provide xml topology, xml mapping, base *.dump, and > trajectory dump files. However, it is not clear how to

Re: [votca] Exclusions in 1.2.4 vs 1.3_rc1

Hi, AFAIR there was a bug in version < 1.3 which cause that only first molecule type was used to generate exclusion lists. If HPC administrator could not upgrade VOTCA the you have to install your own local copy (which is a pretty straightforward procedure). Best, Jakub On 7 December 2015 at

Re: [votca] Mapping.xml for a long polymer chain

t http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout. #!/usr/bin/env python """ Copyright (C) 2015 Jakub Krajniak <jkrajn...@gmail.com> This file is distributed under free software licence: you can redistribute it and/or modify it

[votca] Problem with excluded beads

Dear all, I have noticed that the latest development version (91580e26a728) behaviour in different way than the previous development version (52acb2010494). Mainly I have single 3 beads molecule (hexane) A1-B1-A2 with bonds A1-B1, A2-B2 and angle A1-B1-A2; I expected that csg_stat will not

Re: [votca] Problem with excluded beads

On 27 April 2015 at 16:57, Christoph Junghans jungh...@votca.org wrote: 2015-04-27 4:10 GMT-06:00 Jakub Krajniak jkrajn...@gmail.com: Dear all, I have noticed that the latest development version (91580e26a728) behaviour in different way than the previous development version

[votca] Can thermoforce be calculated not only with Gromacs?

Hi, Am I right that calculating thermoforce can only be done with GROMACS engine? I tried to simply say programespressopp/program but immediately I get an error with statement of missing grompp.mdp file. Are there some significant reason to not use other md engine (like Espresso++) ? Best,

[votca] Running external commands

Dear, I tried to find it in documentation but without success. So I thought about to run some command at the begging of the step and at the end of it. That could be any bash/python/software piece of code. Is it possible with the current state of the code? Best, Jakub -- You received this

[votca] Theromodynamic force - xsplit scheme

in that case? Best, Jakub Krajniak -- Jakub Krajniak, Computer Science Department @ KU Leuven -- 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+unsubscr

Re: [votca] Coarse-graining short polymer, problems

that. Is it possible that it is because of bond interaction? I have defined the exclusion list for .top so this should be handled and the behavior does not changed. Best regards, Jakub Krajniak -- You received this message because you are subscribed to the Google Groups votca group. To unsubscribe from

Re: [votca] Coarse-graining short polymer, problems

(...) And the convergence, I have add post_addconvergence/post_add so that I can measure the convergence. 4. What should be the optimal case for the convergence? What I am getting: (step_001: ~300, step_002: ~232, step_003: ~133) and then suddenly for step_004 it is ~8000.

Re: [votca] Coarse-graining short polymer, problems

On Sunday, 26 January 2014 21:02:58 UTC+1, Christoph Junghans wrote: 2014-01-26 Jakub Krajniak jkra...@gmail.com javascript:: (...) And the convergence, I have add post_addconvergence/post_add so that I can measure the convergence. 4. What should be the optimal case

Re: [votca] Coarse-graining short polymer, problems

On Tuesday, 21 January 2014 17:24:36 UTC+1, Christoph Junghans wrote: 2014/1/21 Jakub Krajniak jkra...@gmail.com javascript:: Hi all, I am playing with Votca from a couple of weeks to get the effective potential of quite simple polymer system. Mainly I have very short (4 beads

[votca] Re: Coarse-graining short polymer, problems

Forgot to mention. I'd like to get the potential for non-bonded interaction by using the iterative Boltzmann method. Best, Jakub -- 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

Re: [votca] What is a DUM residue name in the pdb reader

, Jakub Krajniak -- 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

[votca] What is a DUM residue name in the pdb reader

. Best, Jakub Krajniak -- 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+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit