[gmx-users] Neutralizing

[mohammad r]

Thank you Parham and Justin,
Excuse me I have another question, in simulation of a water-peptide system, is it necessary to use QM/MM simulation during the entire process? Because I didn't see it in the tutorials. By the way I generated the pdb file by using charmm-gui then import it in amber to get the topology and coordinate files, finally I converted the topology and coordinate files to gromacs format and did the rest of simulation by gromacs. but I didn't run QM/MM simulation. Does it make trouble in the results?
Best, Mohammad. 

    On Wednesday, March 9, 2016 4:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
 

 

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) <pjabbarzadeh at 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.
> ​​​​​​======​======​=============
> ​PhD candidate - Lecturer in drug discovery
> Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia
> ​======​===================Publication ::: Featured Publication ::: Website ::: FaceBook
> On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0325 at 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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