Hi
I would like to change the temperature of the simulation (NPT.mdp) inside
my bash script, any one has idea?
thanks
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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.
This is a welcoming and friendly community, with somewhat busy but still
nice people. The manual is available at:
http://manual.gromacs.org/documentation/
One can search for temperature information here:
http://manual.gromacs.org/documentation/current/reference-manual/index.html
to find :
Dear all,
I am going to use Gromacs/ORCA interface for QM/MM calculation in the
metalloenzyme model. I have done some QMMM calculations with other
interface (AMBER/TURBOMOLE) I am also familiar with QM in ORCA but new
user of Gromacs!
I could get general overview how this feature works in
my question for you: have you ever read gromacs manual/documentation?
On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy wrote:
> Hi
>
> I would like to change the temperature of the simulation (NPT.mdp) inside
> my bash script, any one has idea?
> thanks
> --
> Gromacs Users mailing list
>
> * Please
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 wrote:
>
>
> On 3/7/19 9:56 AM, Quyen Vu wrote:
> > my question for you: have you ever
Dear gmx comunity,
I have done the following:
-Ran a 100ps simulation and then starting with the same conditions a 30ps
simulation and then restarted upto 100ps.
-If I use -reprod and Nosé hoover thermostat in both trajectories the final
structures match.
-If I use v-rescale it doesn't.
I know
Dear everyone,
My question concerns the effect of the mdp option "vdw-modifier" when vdwtype
is set to user. I have a tabulated 8 - 6 Mie potential and I'm simulating a
coarse grained water, NaCl system, which all interact with the same potential
form but different dispersion coefficients. I
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 wrote:
> Dear all,
> It's my fault that I have un-nice behavior, I'm so sorry for that.
>
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
Dear all
I have simulated a protein-ligand system and the md.xtc and md.gro are now
generated in the output. Unlike my previous simulations of nano systems in
which the .trr trajectory was in the output and the visualization could be done
in an straight forward way of opening the .gro and .trr
a dirty way:
grep -v ref_t npt.mdp >new.mdp && echo -e "ref_t=300" >>new.mdp
sorry again!
On Thu, Mar 7, 2019 at 6:16 PM Amin Rouy wrote:
> 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
You could use a sed command in your script to replace that line, something
like
sed "s/original expression/new expression/" filename -i
But it depends a lot on how your mdp file is formatted in terms of spaces
and tabs.
Hope it helps,
On Thu, 7 Mar 2019, 12:14 Amin Rouy, wrote:
> Hi
>
> I
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