[gmx-users] npt equlibration without position restrain

[Olga Press]

 Dr. Mark Abraham, thank you so much for your help.
That meaning that in the NPT equilibration without position restrains
the refcoord_scaling should not be present at all in the mdp file*?*

Thank you in advance.
Olga

‫בתאריך יום א׳, 20 בינו׳ 2019 ב-11:06 מאת ‪Mark Abraham‬‏ <‪
mark.j.abraham at gmail.com‬‏>:‬

> Hi,
>
> If you're not using position restraints then options that affect how they
> work are inactive.
>
> Mark
>
> On Sun., 20 Jan. 2019, 09:46 Olga Press, <pressol at post.bgu.ac.il> wrote:
>
> > Dear gromacs users,
> >
> >  I perform membrane-protein simulation and used the same mdp files as
> > suggested by the tutorial of Dr. Justin Lemkul with one exception of
> > changing the correct parameters for charmm36ff as suggested
> > by gromacs manual.
> >
> > I performed 10ns of *NVT equilibration with position restrained* on the
> > protein and found a convergence of the temperature to the desired
> > temperature. Followed by 50ns of *NPT equilibration with position
> > restrained *on the protein, and after that,  I performed 100ns of *NPT
> > equilibration without position restraint*.
> > My question is, in the *NPT equilibration without the position restrain,*
> > what should I put in the category of   *refcoord_scaling? com? *or
> should I
> > delete it as I found in the MD.mdp file in the tutorial?
> >
> > Thanks in advance,
> > Olga
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