Re: [gmx-users] Restarting crashed simmulation.

Thanks sir Justin and sir Mark On Sat, 12 May 2018 3:27 pm Mark Abraham, wrote: > Hi, > > Or use the existing tool one has for a group of related files, called a > directory or folder ;-) It's not compulsory to do your whole thesis in the > same folder, too :-D > >

Re: [gmx-users] Restarting crashed simmulation.

Hi, Or use the existing tool one has for a group of related files, called a directory or folder ;-) It's not compulsory to do your whole thesis in the same folder, too :-D Mark On Fri, May 11, 2018, 21:01 Justin Lemkul wrote: > > > On 5/11/18 2:11 PM, neelam wafa wrote: > >

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 2:11 PM, neelam wafa wrote: Hi! does this means that i should not have used -deffnm md_0_1 in the run command? Actually I am a student and new to gromacs and have no experties in it. I think I need to read more about md run command options. Use -deffnm, it saves you typing and

Re: [gmx-users] Restarting crashed simmulation.

Hi! does this means that i should not have used -deffnm md_0_1 in the run command? Actually I am a student and new to gromacs and have no experties in it. I think I need to read more about md run command options. Regards On Fri, 11 May 2018 10:57 pm Mark Abraham,

Re: [gmx-users] Restarting crashed simmulation.

Hi, Behaviour has changed since 5.1 to make it harder for this happen, but if you do not call mdrun exactly the same way, older implementations of checkpointing would try to be helpful and sometimes actually not be helpful. This only happens if you try to over manage mdrun. It's best to leave it

Re: [gmx-users] Restarting crashed simmulation.

okay, Thanks On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul wrote: > > > On 5/11/18 1:18 PM, neelam wafa wrote: > >> *This is the message of gmx check for both the trajectories. I*t means >> that >> trajectory is not continuous. Am I right? >> > > They are continuous

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 1:18 PM, neelam wafa wrote: *This is the message of gmx check for both the trajectories. I*t means that trajectory is not continuous. Am I right? They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc starts at the same time) and can be concatenated together. It

Re: [gmx-users] Restarting crashed simmulation.

*This is the message of gmx check for both the trajectories. I*t means that trajectory is not continuous. Am I right? *gmx check -f md_0_1.xtc* Checking file md_0_1.xtc Reading frame 0 time0.000 # Atoms 67864 Precision 0.001 (nm) Reading frame 200 time 2000.000 Item

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 1:12 PM, neelam wafa wrote: The previous command was : gmx mdrun -deffnm md_0_1 I didn't ust -cpi falg . Then the only explanation I can think of for what you are observing is that somehow md_0_1.cpt was not accessible, causing mdrun to start over from t = 0 and write a new

Re: [gmx-users] Restarting crashed simmulation.

The previous command was : gmx mdrun -deffnm md_0_1 I didn't ust -cpi falg . On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul wrote: > > > On 5/11/18 12:52 PM, neelam wafa wrote: > >> I used this command: >> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt >> >> But I think its not

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 12:52 PM, neelam wafa wrote: I used this command: gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt But I think its not appending as new files are being generated with names state.cpt, state_prev.cpt and traj_comp.xtc while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.

Re: [gmx-users] Restarting crashed simmulation.

I used this command: gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt But I think its not appending as new files are being generated with names state.cpt, state_prev.cpt and traj_comp.xtc while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc. Why has it happened ? I have checked log

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 10:42 AM, neelam wafa wrote: Dear Sir Justin! I have restarted the simmulation but its producing a separate log file starting from the step where restarted. Is it normal response or there is some problem with my restart? That shouldn't happen; everything should be appended unless

Re: [gmx-users] Restarting crashed simmulation.

Dear Sir Justin! I have restarted the simmulation but its producing a separate log file starting from the step where restarted. Is it normal response or there is some problem with my restart? Thanks in advance. On Fri, May 11, 2018 at 12:06 PM, neelam wafa wrote: >

Re: [gmx-users] Restarting crashed simmulation.

Thanks Sir Justin! I have continued the simmulation from the last step. Regards On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul wrote: > > > On 5/10/18 7:08 AM, neelam wafa wrote: > >> Hi gmx users! >> >> I am running a 5ns md simmulation of a protein with 250 steps. It >>

Re: [gmx-users] Restarting crashed simmulation.

On 5/10/18 7:08 AM, neelam wafa wrote: Hi gmx users! I am running a 5ns md simmulation of a protein with 250 steps. It crashed at 136 steps due to some power problem. Now I want to continue this simmulation. In the manual following command is given: mdrun -s topol.tpr -cpi state.cpt

[gmx-users] Restarting crashed simmulation.

Hi gmx users! I am running a 5ns md simmulation of a protein with 250 steps. It crashed at 136 steps due to some power problem. Now I want to continue this simmulation. In the manual following command is given: mdrun -s topol.tpr -cpi state.cpt but I am confused which file is