On 3/8/16 3:59 AM, mohammad r wrote:
Thank you Parham
You mean that it is not necessary to do QM/MM simulation?
The trivial task of adding ions to neutralize the net charge on the system
certainly does not require anything like QM/MM.
-Justin
On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical
Science) <pjabbarza...@gmail.com> wrote:
Dear Sir
Use this command:
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral
In this case, you don't need the number of ions.
Kind Regards
Parham J. K.
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On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote:
Hi everybody, I’ve generated a water-peptide system, now I want to neutralize
it. Is adding adequate number of ions sufficient for neutralizing process or I
should do QM/MM simulation for the this process? Thank you, Mohammad.
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