[gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

Man Hoang Viet mhviet at ifpan.edu.pl
Tue Dec 15 22:11:11 CET 2015


> Date: Tue, 15 Dec 2015 13:55:08 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] amber force field ff12SB and ff14SB for
> 	gromacs uploaded
> Message-ID: <5670620C.6040903 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> On 12/15/15 1:52 PM, Man Hoang Viet wrote:

> The concern is less about the method of conversion; these types of
> programs are
> reasonably straightforward to write.  The concern is always that the
> energies
> and forces calculated in one program match the other.  The simplest thing
> to do
> is run some single-point energy evaluations in AMBER and GROMACS.  If they
> match, your conversion is successful.  If they don't, you have a problem
> with
> the integrity of the GROMACS files.  You say above that you "make sure
> that they
> are the same in AMBER and GROMACS" but you don't specify what that means.
> Visual inspection of the contents?  Or actual quantitative assessment?
> -Justin

Yes, I just try to show to Alexey Shvetsov or some gromas users who want
to do check the conversion. It is too much thing to post for the detail of
residue comparing. I agree with your suggestion about testing. I will try
to do test and report it as soon as possible. Here I really want other
gromacs users do check my conversion and take apart the testing to make
the conversion completely successful. It will give us more freedom in
doing with GROMACS.

> Date: Tue, 15 Dec 2015 20:36:52 +0100
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users

> Why is documentation not important, could you elaborate?

I just mean it does not effect on gromacs running. I know it is very
important to authorized information.

> Note that the Makefiles are outdated too, I suggest either fixing them or
> removing them.

Thank you for your comment, I fixed it.

> Plus, you seem to have left no contact information in the tarball either
> which (together with the unclear verification process), I'd say, makes the
> FF port risky to use.

I work alone in the conversion that why I wish other users do check and
test the FF together. I hope coming tests will remove the risky and we
will have the new FF in GROMACS.

Viet Man

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