[gmx-users] Coarse grained: non bonded interactions via iterative Boltzmann inversion

Dear all,   I have  some questions regarding the parametrisation of the non bonded interactions when performing coarse grained simulations. I would like to use the iterative Boltzmann inversion (IBI)  to identify the right non bonded interaction potentials.   Is it necessary to calculate the

[gmx-users] Rotation of the molecule

Dear all,   Is it possible to remove the rotation of a molecule? I found the mdp option: "comm_mode = Angular" and tried it but I am not sure wheather I can use this option with my system: I am considering a very long chain (~300 monomers) . I performed coase graining and simulated the

Re: [gmx-users] tabulated potential - problem

Sorry, I forgot to change the caption.   Gesendet: Montag, 07. September 2015 um 18:14 Uhr Von: "Liz Bell" <lizb...@gmx.at> An: gmx-us...@gromacs.org Betreff: [gmx-users] tabulated potential - problem Dear all,   Is there a possibility to plot the intramolecular ene

[gmx-users] tabulated potential - problem

Dear all,   Is there a possibility to plot the intramolecular energy terms?   3. of "Diagnosing an Unstable System" of the page   http://www.gromacs.org/Documentation/Terminology/Blowing_Up   sounds as if this is possible. Gmx energy only shows the interaction energys of the energy groups

[gmx-users] Blowing Up - intramolecular energy terms

Dear all, Is there a possibility to plot the intramolecular energy terms?   3. of "Diagnosing an Unstable System" of the page   http://www.gromacs.org/Documentation/Terminology/Blowing_Up   sounds as if this is possible. Gmx energy only shows the non bonded interaction energys of the

Re: [gmx-users] tabulated potential - problem

users] tabulated potential - problem On 9/7/15 12:14 PM, Liz Bell wrote: > Dear all, > Is there a possibility to plot the intramolecular energy terms? > 3. of "Diagnosing an Unstable System" of the page > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > sounds as i

Re: [gmx-users] tabulated potential - problem

n 9/7/15 1:04 PM, Liz Bell wrote: > Sorry I did not know how to deal with the fact that I posted my question with a > wrong topic. > Thank you for your answer. But I do not really understand what you mean. My > topology contains those things like > bond, angle and dihedral terms: > [

[gmx-users] tabulated potential - problem

Dear all, I have a question about the handling of the tabulated interactions. I am using tabulated potentials for my simulations. With grompp there is no problem, i.e. no error messages. Running mdrun produces: Fatal error: A tabulated bond interaction table number 1 is out of the table

[gmx-users] tabulated bonded interaction functions - problem with the forces

Dear all, I have a question concerning tabulated potentials: My System consists of three different particles P_1, P_2 and P_3 and I would like to use tabulated potentials for the bonded as well as the nonbonded interactions. Runing mdrun produces both: 1.) various warnings: WARNING: For

Re: [gmx-users] tabulated bonded interaction functions

of it. Thanks, Mark On Tue, Aug 4, 2015 at 3:55 PM Liz Bell lizb...@gmx.at wrote: Thank you for your response. The column Order of parameters and their units of table 5.5 states that I have to include a value for n and the force constant k. I tried it by simply setting k to 1: [ bonds ] ;ai aj

Re: [gmx-users] tabulated bonded interaction functions

mark.j.abra...@gmail.com An:gmx-us...@gromacs.org Betreff:Re: [gmx-users] tabulated bonded interaction functions Hi, Yes you have to specify k. That detail is in table 5.5, to which that section refers you. Mark On Tue, Aug 4, 2015 at 3:26 PM Liz Bell lizb...@gmx.at wrote: Dear all

Re: [gmx-users] tabulated bonded interaction functions

Dear all, Regarding my question concerning the format of the [bonds] part of the topology file, I tried some new things: Changing the [bonds] part in the topology to: [ bonds ] ;ai aj func n 1 2 9 0 for n=0 (and therefore the file: table_b0.xvg) produces this error message: Fatal

[gmx-users] tabulated bonded interaction functions

Dear all, I am perfoming MD simulations of P3Ht chains and I would like to define the bonded as well as the nonbonded parameters using tables. Regarding the bonded parameters, there are no problems until now, as I simply wrote some additional lines in the mdp file (similar to this explanation: