Hello
If you only need the parameters of the molecules (e.g. list of bond, atom
masses and charges) you could build a fake tpr with a minimal list of
parameters (for instance used for minimization) and use an the desired old
version of grompp (Gromacs 5.0.3).
Stéphane
On 9/26/19 10:26 AM, Neena Susan Eappen wrote:
Hi Justin,
This is the actual error message,
Residue 3 named ALA of a molecule in the input file was mapped to an entry in
the topology database, but the atom C used in that entry is not found in the
input file. Perhaps your atom and/or
Hi Justin,
This is the actual error message,
Residue 3 named ALA of a molecule in the input file was mapped to an entry in
the topology database, but the atom C used in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be fixed.
I was trying to add a
> Am 26.09.2019 um 16:24 schrieb Harutyun Sahakyan :
>
> Dear Gromacs users,
>
> Computational electrophysiology protocol has some analyzing tools allowing
> to count ion flux etc. I have used an external electric field to simulate
> the process of ion permissions through a membrane channel.
Dear all,
I am doing alchemical transformation free energy calculation. Grompp
offers the option to provide a position restrain file for state B via
-rb flag. Can I use this for free energy calculations if I want to
restrain the coordinates in state B to different positions? If yes, does
Dear Gromacs users,
Computational electrophysiology protocol has some analyzing tools allowing
to count ion flux etc. I have used an external electric field to simulate
the process of ion permissions through a membrane channel. How can I count
ion flux, conductivity or something like that?
Best
Hi Carsten,
Thank you for replying,
Is it possible to set CompEL for a non-double channel system? Without
rising ions disbalance, just for counting. I could use a piece of CompEL
code to modify it for ion flux counting, maybe you have any suggestions?
Harut
On Thu, Sep 26, 2019 at 6:36 PM
