Re: Fw: Fw: [gmx-users] How to restart the crashed run

2013-09-17 Thread Justin Lemkul
On 9/17/13 5:58 AM, Mahboobeh Eslami wrote: dear mark will all my output write well after restart and are their names md? will old my output reconstruct or will generate new output? The default behavior of mdrun is to append to existing files. Otherwise, you can use -noappend to get a new

Fw: Fw: [gmx-users] How to restart the crashed run

2013-09-17 Thread Mahboobeh Eslami
: Fw: [gmx-users] How to restart the crashed run dear mark thank you so much Good luck - Forwarded Message - From: Mark Abraham To: Mahboobeh Eslami ; Discussion list for GROMACS users Sent: Tuesday, September 17, 2013 1:21 PM Subject: Re: Fw: [gmx-users] How to restart the c

Fw: Fw: [gmx-users] How to restart the crashed run

2013-09-17 Thread Mahboobeh Eslami
dear mark thank you so much Good luck - Forwarded Message - From: Mark Abraham To: Mahboobeh Eslami ; Discussion list for GROMACS users Sent: Tuesday, September 17, 2013 1:21 PM Subject: Re: Fw: [gmx-users] How to restart the crashed run mdrun -v -deffnm md -cpi md IIRC the

Re: Fw: [gmx-users] How to restart the crashed run

2013-09-17 Thread Mark Abraham
t program: >> output files present: md.log >> output files not present or named differently: md.trr md.edr >> >> >> but i have md.trr and md.edr in my folder. >> >> thank you so much >> >> >> - Forwarded Message - >> From

Fw: [gmx-users] How to restart the crashed run

2013-09-17 Thread Mahboobeh Eslami
Mark Abraham To: Mahboobeh Eslami ; Discussion list for GROMACS users Sent: Tuesday, September 17, 2013 12:23 PM Subject: Re: [gmx-users] How to restart the crashed run You named them last time you ran mdrun, either explicitly or with -deffnm. Do the same. Mark On Tue, Sep 17, 2013 at 3:19 AM,

Re: [gmx-users] How to restart the crashed run

2013-09-17 Thread Mark Abraham
edr in my folder. > > thank you so much > > > - Forwarded Message - > From: Mark Abraham > To: Discussion list for GROMACS users > Sent: Tuesday, September 17, 2013 11:22 AM > Subject: Re: [gmx-users] How to restart the crashed run > > > Hi, > > Please ke

[gmx-users] How to restart the crashed run

2013-09-17 Thread Mahboobeh Eslami
t; To: Mahboobeh Eslami ; Discussion list for > GROMACS users > Sent: Tuesday, September 17, 2013 9:36 AM > Subject: Re: [gmx-users] How to restart the crashed run > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests > the 3.x-era restart strategy when check

Re: [gmx-users] How to restart the crashed run

2013-09-16 Thread Mark Abraham
t; To: Mahboobeh Eslami ; Discussion list for > GROMACS users > Sent: Tuesday, September 17, 2013 9:36 AM > Subject: Re: [gmx-users] How to restart the crashed run > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests > the 3.x-era restart strategy when checkpoint files

Re: [gmx-users] How to restart the crashed run

2013-09-16 Thread Mark Abraham
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests the 3.x-era restart strategy when checkpoint files are unavailable. But if you simply have no output files, then you have no ability to restart. Mark On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami wrote: > hi my friends > >

[gmx-users] How to restart the crashed run

2013-09-16 Thread Mahboobeh Eslami
hi my friends please help me i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near the end of the simulation How to restart the crashed run?  in the gromacs.org following comment has been proposed mdrun -s topol.tpr -cpi state.cpt but i don't have state.cpt in my folder.