gromacs.org>
Sent: Thursday, February 8, 2018 9:49 AM
Subject: Re: [gmx-users] Running long MD simulation
And why don't we modify the .mdp file to be protein_and_JZ4 as the same way you
did for water_and_ions instead of making a new index for the list protein_JZ4?
And why do we have
and SOL the same!
Kind Regards,Ahmed Mashaly
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Sunday, February 4, 2018 4:02 PM
Subject: Re: [gmx-users] Running long MD simulation
On 2/4/18 9:57 AM, Ahmed Mashaly wrote:
> And the index file? what is
for thermostatting, energygrps, etc.
-Justin
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Sunday, February 4, 2018 4:20 PM
Subject: Re: [gmx-users] Running long MD simulation
On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
Thanks Justin.
I found this one:
ct: Re: [gmx-users] Running long MD simulation
On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
> Thanks Justin.
>
> I found this one:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html
>
> Another question I have about using cpt
>
>
On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
Thanks Justin.
I found this one:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html
Another question I have about using cpt
I know checkpoint is important for continuing simulation, but I didn't know
that we have to
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Friday, February 2, 2018 5:27 PM
Subject: Re: [gmx-users] Running long MD simulation
On 2/1/18 12:45 PM, Ahmed Mashaly wrote:
> Hi
> I want to run a long MD 200 ns, but I want
On 2/1/18 12:45 PM, Ahmed Mashaly wrote:
Hi
I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be
saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed
It should be very simple with a bash loop and making use of mdrun
-noappend so you avoid
Hi
I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be
saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed
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