[gmx-developers] question about tabulated force field

[Erik Lindahl]

This is not a development question, so please direct it to gmx-users
instead.

To understand differences between Gromacs versions, and in particular why
it's likely a very bad idea to use Gromos force fields, read the release
notes.

Cheers,

Erik

On Thu, Sep 5, 2019 at 11:46 AM Liu, Y. <y.liu at rug.nl> wrote:

> Hi there,
>        I have a question about tabulated force field: what is the
> difference when the tabulated potential and build-in potential are used in
> Gromacs simulations? why they give different results?
>        I simulate a DPPC membrane with Gromos force field. I use standard
> gromos input parameters in the simulation, but the area per lipid (0.630
> (0.008) nm2) is different from when I compute it with tabulated force
> field(0.613 (0.007)nm2). This difference also exist when I use MARTINI
> force field.
>        I have use gmx dump -s *.tpr > comparison.xvg in two cases(build-in
> and tabulated potential) to make sure that the only difference in two
> scenarios is the tabulated potential. Here is the difference:
> <    coulombtype                    = Reaction-Field
> ---
> >    coulombtype                    = User
> 40,41c40,41
> <    epsilon-rf                     = 62
> <    vdw-type                       = Cut-off
> ---
> >    epsilon-rf                     = 1
> >    vdw-type                       = User
> 164c164
> <    tau-t:         0.1         0.1         0.1
> ---
> >    tau-t:        0.01         0.1           1
> 169c169
> <    energygrp-flags[  0]: 0 1
> ---
> >    energygrp-flags[  0]: 2 1
>        Then you may think my tabulated potential is problematic. However,
> I have used Gromacs 4.* with -debug flag to output the tabulated potential.
> Therefore, the tabulated potential should be correct.
>        In the output .edr file, I also found that the tabulated potential
> simulation cannot offer correct temperature for lipids as indicated in the
> thermal stat. At least, with the same parameters, it works well in the
> build-in potential simulation.
>        I do not understand where is the problem and what is the difference
> between the tabulated potential and build-in potential in Gromacs. Maybe it
> use different engine to compute the force?
>         Looking forward to your reply. Thank you.
> regards
> Liuyang
>
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-- 
Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
University
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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