Re: [gmx-users] Running long MD simulation

ubject: 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 some groups duplicated in the default index? for example in the

Re: [gmx-users] Running long MD simulation

water and SOL the same!  Kind Regards,Ahmed Mashaly From: Justin Lemkul 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 the point of i

Re: [gmx-users] Running long MD simulation

thermostatting, energygrps, etc. -Justin From: Justin Lemkul 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: https://mailman-1.sys.kth.se

Re: [gmx-users] Running long MD simulation

And the index file? what is the point of inserting them as input for NPT and MD? They should be for the whole system, not certain groups, right? Kind Regards,Ahmed From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Sunday, February 4, 2018 4:20 PM Subject: Re: [gmx-users] Running

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 I know checkpoint is important for continuing simulation, but I didn't know that we have to

Re: [gmx-users] Running long MD simulation

Ahmed From: Justin Lemkul 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 the outputs of ev

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 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 namin

[gmx-users] Running long MD simulation

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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!