[gmx-users] script

[Amin Rouy]

It is fine.
My question was not about '.mdp' itself. I meant how to define the
'Temperature' inside the bash scrip, to avoid changing it by opening the
.mdp file.


On Thu, Mar 7, 2019 at 4:57 PM Quyen Vu <vuqv.phys at gmail.com> wrote:

> Dear all,
> It's my fault that I have un-nice behavior, I'm so sorry for that.
> If I understand correctly, you are working with Gromacs so you should
> understand what is the .mdp file used for and there, the document of
> temperature section talk about that.
>
>
> On Thu, Mar 7, 2019 at 4:06 PM Amin Rouy <aminrou1986 at gmail.com> wrote:
>
> > Thank you Justin.
> >
> > Yes, Quyen I've read the manual. I got helps from Justin's scrips in his
> > tutorial page (great source) and googled before I came to write here.
> >
> >
> > On Thu, Mar 7, 2019 at 4:01 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 3/7/19 9:56 AM, Quyen Vu wrote:
> > > > my question for you: have you ever read gromacs manual/documentation?
> > >
> > > Where in the GROMACS manual do we discuss how to use Linux commands to
> > > alter scripts in this way? Please do not simply dismiss others'
> > > questions; it is not productive and not helpful. There are legitimate
> > > cases of users not utilizing documentation and web searching, but I
> > > would argue this is not one of them.
> > >
> > > > On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy <aminrou1986 at gmail.com>
> > wrote:
> > > >
> > > >> Hi
> > > >>
> > > >> I would like to change the temperature of the simulation (NPT.mdp)
> > > inside
> > > >> my bash script, any one has idea?
> > >
> > > You can make replacements in files using standard Linux utilities like
> > > sed, in conjunction with others like grep and awk. This isn't a
> > > GROMACS-specific issue, so I'd suggest looking at more general Linux
> > > forums.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Office: 301 Fralin Hall
> > > Lab: 303 Engel Hall
> > >
> > > Virginia Tech Department of Biochemistry
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.thelemkullab.com
> > >
> > > ==================================================
> > >
> > > --
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