Re: [gmx-users] Restarting simulation -s. files?

I see, Thank you for the information Justin. On Sep 28, 2013, at 2:57 PM, Justin Lemkul wrote: > > > On 9/28/13 2:52 PM, Xu Dong Huang wrote: >> Justin, >> >> I see. Is there a way to *stitch* the two files together so I can continue >> onto a NPT run? >> > > Appending is the default beh

Re: [gmx-users] Restarting simulation -s. files?

On 9/28/13 2:52 PM, Xu Dong Huang wrote: Justin, I see. Is there a way to *stitch* the two files together so I can continue onto a NPT run? Appending is the default behavior of mdrun, if invoked properly and the files haven't been messed with. If not, trjcat appends trajectories and enec

Re: [gmx-users] Restarting simulation -s. files?

Justin, I see. Is there a way to *stitch* the two files together so I can continue onto a NPT run? On Sep 28, 2013, at 2:49 PM, Justin Lemkul wrote: > > > On 9/28/13 2:46 PM, Xu Dong Huang wrote: >> Hello gromacs users, >> >> I restarted my run due to power failure using mdrun -v -s .t

Re: [gmx-users] Restarting simulation -s. files?

On 9/28/13 2:46 PM, Xu Dong Huang wrote: Hello gromacs users, I restarted my run due to power failure using mdrun -v -s .tpr -cpi .cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make it so it continues to update the original .xtc and .tpr files? If you're ge

[gmx-users] Restarting simulation -s. files?

Hello gromacs users, I restarted my run due to power failure using mdrun -v -s .tpr -cpi .cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make it so it continues to update the original .xtc and .tpr files? Thanks, Xu Huang Research Assistant Chemical & Biochemica

Re: [gmx-users] Restarting simulation

On 2/8/13 12:31 AM, James Starlight wrote: Dear Gromacs Users! I try to restart canceled (by cnttl+z) simulation using cpt file mdrun -v -deffnm md_b2ar_APO -cpi md_b2ar_APO_prev after this I obtain error like Checksum wrong for 'md_b2ar_APO.log'. The file has been replaced or its conten

Re: [gmx-users] restarting simulation after segmentation fault

On 5/8/12 11:40 AM, Za Pour wrote: Dear gmx users I am simulating a system involving carbon nanotube. I successfully completed the EM,NVT and NPT equilibration phase and then started to run production simulation(NVT ensemble) for 10 ns.However, after passing more than 50 steps(1 ns),I gave

[gmx-users] restarting simulation after segmentation fault

Dear gmx users I am simulating a system involving carbon nanotube. I successfully completed the EM,NVT and NPT equilibration phase and then started to run production  simulation(NVT ensemble) for 10 ns.However, after passing more than 50 steps(1 ns),I gave the segmentation error.I investigated

Re: [gmx-users] restarting simulation

Thanks guys XAvier Periole wrote: > > On Jun 11, 2010, at 3:30 PM, Gavin Melaugh wrote: > >> Hi all >> >> For restarting a crashed simulation, do you have to use the -s topol.tpr >> in the command below. I have left it out and everything seems to be O.K. >> I'm just double checking though. >> >> m

Re: [gmx-users] restarting simulation

Gavin Melaugh wrote: Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append If you're using default filenames, if you

Re: [gmx-users] restarting simulation

On Jun 11, 2010, at 3:30 PM, Gavin Melaugh wrote: Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append -s topol.t

[gmx-users] restarting simulation

Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append -- gmx-users mailing listgmx-users@gromacs.org http://lists.