[gmx-users] Ignoring H-atoms.
zebamir85 at gmail.com
Tue Feb 7 08:35:58 CET 2017
f igoring h-atom command is applied ,,then forcefield will ignore all the
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.
On Mon, Feb 6, 2017 at 10:12 PM, maria khan <mariabiochemist1 at gmail.com>
> 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.
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