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
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
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
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
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
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
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:
> [
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
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
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
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
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
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:
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