mohammad.r0325 at yahoo.com
Wed Mar 9 07:48:54 CET 2016
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?
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.
> 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
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