[gmx-users] npt equlibration without position restrain

[Olga Press]

Thank you very much for your help.

Olga

‫בתאריך יום א׳, 20 בינו׳ 2019 ב-22:35 מאת ‪Mark Abraham‬‏ <‪
mark.j.abraham at gmail.com‬‏>:‬

> Hi,
>
> They're inactive so whether they have any value or are present does not
> matter.
>
> Mark
>
> On Sun., 20 Jan. 2019, 10:34 Olga Press, <pressol at post.bgu.ac.il> wrote:
>
> >  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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