[gmx-users] Ignoring H-atoms.

[Amir Zeb]

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.

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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