Re: [gmx-users] Running long MD simulation

2018-02-08 Thread Ahmed Mashaly
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

Re: [gmx-users] Running long MD simulation

2018-02-08 Thread Ahmed Mashaly
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

Re: [gmx-users] Running long MD simulation

2018-02-04 Thread Justin Lemkul
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:

Re: [gmx-users] Running long MD simulation

2018-02-04 Thread Ahmed Mashaly
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 > >

Re: [gmx-users] Running long MD simulation

2018-02-04 Thread Justin Lemkul
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

Re: [gmx-users] Running long MD simulation

2018-02-04 Thread Ahmed Mashaly
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

Re: [gmx-users] Running long MD simulation

2018-02-02 Thread Justin Lemkul
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