Thanks, Pengfei.
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
On Sat, Oct 27, 2018 at 3:33 AM Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Rakesh,
>
> The interaction strength between the carboxylate group and Na+ ion can be
> strong. But you can check the Van der Waals and charge parameters of the
> Na+ ion to make sure you model the system correctly — you can use the
> “printDetails” command in ParmEd to do a quick check.
>
> Hope it helps,
> Pengfei
>
> > On Oct 26, 2018, at 2:25 AM, Rakesh Srivastava <allahabad.21.gmail.com>
> wrote:
> >
> > Hello all,
> >
> > I am doing a simulation of a protein homo-dimer system and what I find
> is a
> > Na+ ion has been stuck at one C-terminal end of one monomer for whole
> > simulation length of 50ns. Should I worry and if yes then what might be
> > possible solutions.
> >
> > Thanks in advance.
> >
> > Rakesh Srivastava
> > Research Fellow
> > School of Computational & Integrative Sciences
> > Jawaharlal Nehru University, New Delhi-110067
> > India
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Received on Fri Oct 26 2018 - 22:00:02 PDT
