[gmx-users] Ignoring H-atoms.

[Amir Zeb]

Thanks Erik,

I got the explanation you kindly posted regarding the posted discussion.

I would like to extend the question that if some one does not flag the
-ignh, so does it mean that the input H-atoms are still there and the force
field will consider them during the rtp file generation?
Further more, if the case is likely not to flag the -ignh, what might be
the possible consequences?

I trust to listen to your precious negotiation.

Cheers!

Amir

On Tue, Feb 7, 2017 at 12:21 AM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

>
>
> > On 7 Feb 2017, at 08:35, Amir Zeb <zebamir85 at gmail.com> wrote:
> >
> > Hello Maria,
> >
> > f igoring h-atom command is applied ,,then forcefield will ignore all the
> > added h-atoms
> >
> > What I know about -ignh flag, it does not mean to remove the h-atoms,
> > alternatively means that during the topology generation, the force field
> is
> > considering the h-atoms as the light atoms and does not pay much
> attention
> > to consider their parameters so accurately.
>
> No. -ignh ignores the hydrogen atoms in the input structure, but uses the
> rtp file(s) to generate new hydrogens. This is useful, for example, when
> some hydrogens are missing in the pdb file. The structure and topology will
> therefore contain hydrogens in the end also with -ignh.
>
> Kind regards,
> Erik
>
> >
> > it would be a vaccum simulation if
> > the h-atom will be ignored
> >
> > Also, in case of vacuum simulation, I think there is no water addition,
> > while here we are gonna adding the water during the salvation step  of
> the
> > procedure. So, I think you don't need to worry about it.
> >
> > At the end, I would like to appraise in deep the explanation of other
> users.
> >
> > Cheers!
> >
> > Amir
> >
> > On Mon, Feb 6, 2017 at 10:12 PM, maria khan <mariabiochemist1 at gmail.com>
> > wrote:
> >
> >> Dear Gromacs users,,
> >>
> >> if igoring h-atom command is applied ,,then forcefield will ignore all
> the
> >> added h-atoms,,,so my question is then it would be a vaccum simulation
> if
> >> the h-atom will be ignored,,secondly the results will be also differnt
> then
> >> when h-atoms are considered.
> >>
> >> Regards..
> >> --
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