[gmx-users] Ignoring H-atoms.

[Erik Marklund]

> 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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