Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

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
>
> Mark
>
> On Fri, May 11, 2018, 21:01 Justin Lemkul  wrote:
>
> >
> >
> > 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 makes your life easier, because
> > instead of relying on generic, default file names, you know exactly what
> > you did and what your files hold.
> >
> > -Justin
> >
> > > Regards
> > >
> > > On Fri, 11 May 2018 10:57 pm Mark Abraham, 
> > wrote:
> > >
> > >> 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 alone to append with default file names, or use -noappend
> with
> > >> default filenames and get the part number added automatically. But if
> > you
> > >> want to change the filenames to have a part number you manage
> yourself,
> > you
> > >> have to manage everything else too...
> > >>
> > >> Mark
> > >>
> > >> On Fri, May 11, 2018 at 7:28 PM neelam wafa 
> > wrote:
> > >>
> > >>> 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 (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
> > >>> starts
> >  at the same time) and can be concatenated together. It appears your
> > run
> > >>> did
> >  continue from the checkpoint file. I have no explanation for why the
> > >> file
> >  names are not what one would expect.
> > 
> >  -Justin
> > 
> >  *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#frames Timestep (ps)
> > > Step   27310
> > > Time   27310
> > > Lambda   0
> > > Coords 27310
> > > Velocities   0
> > > Forces   0
> > > Box27310
> > >
> > > * gmx check -f traj_comp.xtc*
> > >
> > >
> > > Checking file traj_comp.xtc
> > > Reading frame   0 time 2720.000
> > > # Atoms  67864
> > > Precision 0.001 (nm)
> > > Last frame 13 time 2850.000
> > >
> > >
> > > Item#frames Timestep (ps)
> > > Step1410
> > > Time1410
> > > Lambda   0
> > > Coords  1410
> > > Velocities   0
> > > Forces   0
> > > Box 1410
> > >
> > >
> > > On Fri, May 11, 2018 at 5:12 PM, neelam wafa <
> neelam.w...@gmail.com>
> > > wrote:
> > >
> > > 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 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 files but not able to
> > >> infer
> > >>> a
> >  proper answer.
> > 
> >  The file names are contained within the .cpt file, and those are
> > >> what
> > >>> will be written. You haven't said what your previous command was,
> > >> but
> > >>> the
> > >>> use of -deffnm makes this much easier:
> > >>>
> > >>> gmx mdrun -deffnm md_0_1 -cpi
> > >>>
> > >>> You will always get clearly named files.
> > >>>
> > >>> If its not appened, will the final trajectory .xtc obtained cover
> > >> the
> >  whole
> >  simmulation or I ll have to combine both results?

Re: [gmx-users] Restarting crashed simmulation.

[Mark Abraham]

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:
> > 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 makes your life easier, because
> instead of relying on generic, default file names, you know exactly what
> you did and what your files hold.
>
> -Justin
>
> > Regards
> >
> > On Fri, 11 May 2018 10:57 pm Mark Abraham, 
> wrote:
> >
> >> 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 alone to append with default file names, or use -noappend with
> >> default filenames and get the part number added automatically. But if
> you
> >> want to change the filenames to have a part number you manage yourself,
> you
> >> have to manage everything else too...
> >>
> >> Mark
> >>
> >> On Fri, May 11, 2018 at 7:28 PM neelam wafa 
> wrote:
> >>
> >>> 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 (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
> >>> starts
>  at the same time) and can be concatenated together. It appears your
> run
> >>> did
>  continue from the checkpoint file. I have no explanation for why the
> >> file
>  names are not what one would expect.
> 
>  -Justin
> 
>  *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#frames Timestep (ps)
> > Step   27310
> > Time   27310
> > Lambda   0
> > Coords 27310
> > Velocities   0
> > Forces   0
> > Box27310
> >
> > * gmx check -f traj_comp.xtc*
> >
> >
> > Checking file traj_comp.xtc
> > Reading frame   0 time 2720.000
> > # Atoms  67864
> > Precision 0.001 (nm)
> > Last frame 13 time 2850.000
> >
> >
> > Item#frames Timestep (ps)
> > Step1410
> > Time1410
> > Lambda   0
> > Coords  1410
> > Velocities   0
> > Forces   0
> > Box 1410
> >
> >
> > On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
> > wrote:
> >
> > 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 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 files but not able to
> >> infer
> >>> a
>  proper answer.
> 
>  The file names are contained within the .cpt file, and those are
> >> what
> >>> will be written. You haven't said what your previous command was,
> >> but
> >>> the
> >>> use of -deffnm makes this much easier:
> >>>
> >>> gmx mdrun -deffnm md_0_1 -cpi
> >>>
> >>> You will always get clearly named files.
> >>>
> >>> If its not appened, will the final trajectory .xtc obtained cover
> >> the
>  whole
>  simmulation or I ll have to combine both results?
> 
>  Use gmx check.
> >>> -Justin
> >>>
> >>>
> >>> Regards
> >>>
>  On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
>  wrote:
> 
> 
>  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
> 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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 makes your life easier, because 
instead of relying on generic, default file names, you know exactly what 
you did and what your files hold.


-Justin


Regards

On Fri, 11 May 2018 10:57 pm Mark Abraham,  wrote:


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 alone to append with default file names, or use -noappend with
default filenames and get the part number added automatically. But if you
want to change the filenames to have a part number you manage yourself, you
have to manage everything else too...

Mark

On Fri, May 11, 2018 at 7:28 PM neelam wafa  wrote:


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 (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc

starts

at the same time) and can be concatenated together. It appears your run

did

continue from the checkpoint file. I have no explanation for why the

file

names are not what one would expect.

-Justin

*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#frames Timestep (ps)
Step   27310
Time   27310
Lambda   0
Coords 27310
Velocities   0
Forces   0
Box27310

* gmx check -f traj_comp.xtc*


Checking file traj_comp.xtc
Reading frame   0 time 2720.000
# Atoms  67864
Precision 0.001 (nm)
Last frame 13 time 2850.000


Item#frames Timestep (ps)
Step1410
Time1410
Lambda   0
Coords  1410
Velocities   0
Forces   0
Box 1410


On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
wrote:

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 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 files but not able to

infer

a

proper answer.

The file names are contained within the .cpt file, and those are

what

will be written. You haven't said what your previous command was,

but

the
use of -deffnm makes this much easier:

gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.

If its not appened, will the final trajectory .xtc obtained cover

the

whole
simmulation or I ll have to combine both results?

Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
wrote:


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 there

was

some
problem (check the .log file itself and stdout/stderr for

messages).

Appending is for convenience but there is no functional

requirement

for
it
(I never append on the fly by personal preference, I just

concatenate

later).

-Justin


Thanks in advance.

On Fri, May 11, 2018 at 12:06 PM, neelam wafa <

neelam.w...@gmail.com>

wrote:

Thanks Sir Justin!

I have continued the simmulation from the last step.

Regards

On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <

jalem...@vt.edu>

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
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 state.cpt. I have got two cpt
files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their

contents

with

gmx

check. You will see an obvious difference in what they contain.
Also
consult the mdrun help info, which specifically addresses your
question.

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

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,  wrote:

> 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 alone to append with default file names, or use -noappend with
> default filenames and get the part number added automatically. But if you
> want to change the filenames to have a part number you manage yourself, you
> have to manage everything else too...
>
> Mark
>
> On Fri, May 11, 2018 at 7:28 PM neelam wafa  wrote:
>
> > 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 (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
> > starts
> > > at the same time) and can be concatenated together. It appears your run
> > did
> > > continue from the checkpoint file. I have no explanation for why the
> file
> > > names are not what one would expect.
> > >
> > > -Justin
> > >
> > > *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#frames Timestep (ps)
> > >> Step   27310
> > >> Time   27310
> > >> Lambda   0
> > >> Coords 27310
> > >> Velocities   0
> > >> Forces   0
> > >> Box27310
> > >>
> > >> * gmx check -f traj_comp.xtc*
> > >>
> > >>
> > >> Checking file traj_comp.xtc
> > >> Reading frame   0 time 2720.000
> > >> # Atoms  67864
> > >> Precision 0.001 (nm)
> > >> Last frame 13 time 2850.000
> > >>
> > >>
> > >> Item#frames Timestep (ps)
> > >> Step1410
> > >> Time1410
> > >> Lambda   0
> > >> Coords  1410
> > >> Velocities   0
> > >> Forces   0
> > >> Box 1410
> > >>
> > >>
> > >> On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
> > >> wrote:
> > >>
> > >> 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 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 files but not able to
> infer
> > a
> > > proper answer.
> > >
> > > The file names are contained within the .cpt file, and those are
> what
> >  will be written. You haven't said what your previous command was,
> but
> >  the
> >  use of -deffnm makes this much easier:
> > 
> >  gmx mdrun -deffnm md_0_1 -cpi
> > 
> >  You will always get clearly named files.
> > 
> >  If its not appened, will the final trajectory .xtc obtained cover
> the
> > 
> > > whole
> > > simmulation or I ll have to combine both results?
> > >
> > > Use gmx check.
> > 
> >  -Justin
> > 
> > 
> >  Regards
> > 
> > >
> > > On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
> > > wrote:
> > >
> > >
> > > 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 there
> > was
> > >>>
> > >> some
> > >> problem (check the .log file itself and stdout/stderr for
> messages).
> > >> Appending is for convenience but there is no functional
> requirement
> > >> for
> > >> it
> > >> (I never append on the fly by personal preference, I just
> > concatenate
> > >> later).
> > >>
> > >> -Justin
> > >>
> > >>
> > >> Thanks in advance.
> > 

Re: [gmx-users] Restarting crashed simmulation.

[Mark Abraham]

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 alone to append with default file names, or use -noappend with
default filenames and get the part number added automatically. But if you
want to change the filenames to have a part number you manage yourself, you
have to manage everything else too...

Mark

On Fri, May 11, 2018 at 7:28 PM neelam wafa  wrote:

> 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 (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
> starts
> > at the same time) and can be concatenated together. It appears your run
> did
> > continue from the checkpoint file. I have no explanation for why the file
> > names are not what one would expect.
> >
> > -Justin
> >
> > *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#frames Timestep (ps)
> >> Step   27310
> >> Time   27310
> >> Lambda   0
> >> Coords 27310
> >> Velocities   0
> >> Forces   0
> >> Box27310
> >>
> >> * gmx check -f traj_comp.xtc*
> >>
> >>
> >> Checking file traj_comp.xtc
> >> Reading frame   0 time 2720.000
> >> # Atoms  67864
> >> Precision 0.001 (nm)
> >> Last frame 13 time 2850.000
> >>
> >>
> >> Item#frames Timestep (ps)
> >> Step1410
> >> Time1410
> >> Lambda   0
> >> Coords  1410
> >> Velocities   0
> >> Forces   0
> >> Box 1410
> >>
> >>
> >> On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
> >> wrote:
> >>
> >> 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 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 files but not able to infer
> a
> > proper answer.
> >
> > The file names are contained within the .cpt file, and those are what
>  will be written. You haven't said what your previous command was, but
>  the
>  use of -deffnm makes this much easier:
> 
>  gmx mdrun -deffnm md_0_1 -cpi
> 
>  You will always get clearly named files.
> 
>  If its not appened, will the final trajectory .xtc obtained cover the
> 
> > whole
> > simmulation or I ll have to combine both results?
> >
> > Use gmx check.
> 
>  -Justin
> 
> 
>  Regards
> 
> >
> > On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
> > wrote:
> >
> >
> > 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 there
> was
> >>>
> >> some
> >> problem (check the .log file itself and stdout/stderr for messages).
> >> Appending is for convenience but there is no functional requirement
> >> for
> >> it
> >> (I never append on the fly by personal preference, I just
> concatenate
> >> later).
> >>
> >> -Justin
> >>
> >>
> >> Thanks in advance.
> >>
> >> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <
> neelam.w...@gmail.com>
> >>> wrote:
> >>>
> >>> 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
> >> crashed at  136 steps due to some 

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

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 (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc starts
> at the same time) and can be concatenated together. It appears your run did
> continue from the checkpoint file. I have no explanation for why the file
> names are not what one would expect.
>
> -Justin
>
> *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#frames Timestep (ps)
>> Step   27310
>> Time   27310
>> Lambda   0
>> Coords 27310
>> Velocities   0
>> Forces   0
>> Box27310
>>
>> * gmx check -f traj_comp.xtc*
>>
>>
>> Checking file traj_comp.xtc
>> Reading frame   0 time 2720.000
>> # Atoms  67864
>> Precision 0.001 (nm)
>> Last frame 13 time 2850.000
>>
>>
>> Item#frames Timestep (ps)
>> Step1410
>> Time1410
>> Lambda   0
>> Coords  1410
>> Velocities   0
>> Forces   0
>> Box 1410
>>
>>
>> On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
>> wrote:
>>
>> 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 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 files but not able to infer a
> proper answer.
>
> The file names are contained within the .cpt file, and those are what
 will be written. You haven't said what your previous command was, but
 the
 use of -deffnm makes this much easier:

 gmx mdrun -deffnm md_0_1 -cpi

 You will always get clearly named files.

 If its not appened, will the final trajectory .xtc obtained cover the

> whole
> simmulation or I ll have to combine both results?
>
> Use gmx check.

 -Justin


 Regards

>
> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
> wrote:
>
>
> 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 there was
>>>
>> some
>> problem (check the .log file itself and stdout/stderr for messages).
>> Appending is for convenience but there is no functional requirement
>> for
>> it
>> (I never append on the fly by personal preference, I just concatenate
>> later).
>>
>> -Justin
>>
>>
>> Thanks in advance.
>>
>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
>>> wrote:
>>>
>>> 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
>> 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 state.cpt. I have got two cpt
>> files
>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>
>> Look at the time stamps of the files and inspect their contents
>> with
>>
>> gmx
> check. You will see an obvious difference in what they contain.
> Also
> consult the mdrun help info, which specifically addresses your
> question.
>
> Also I did not get a md_1_0.gro file/ Is is due to incomplete
> simmulation?
> Yes, because that file is only produced from the last step.
>
> Also do I need to specify  -append flag or not? I am using version
> 5.1.5
> -append has been the 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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 appears 
your run did continue from the checkpoint file. I have no explanation 
for why the file names are not what one would expect.


-Justin


*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#frames Timestep (ps)
Step   27310
Time   27310
Lambda   0
Coords 27310
Velocities   0
Forces   0
Box27310

* gmx check -f traj_comp.xtc*

Checking file traj_comp.xtc
Reading frame   0 time 2720.000
# Atoms  67864
Precision 0.001 (nm)
Last frame 13 time 2850.000


Item#frames Timestep (ps)
Step1410
Time1410
Lambda   0
Coords  1410
Velocities   0
Forces   0
Box 1410


On Fri, May 11, 2018 at 5:12 PM, neelam wafa  wrote:


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 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 files but not able to infer a
proper answer.


The file names are contained within the .cpt file, and those are what
will be written. You haven't said what your previous command was, but the
use of -deffnm makes this much easier:

gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.

If its not appened, will the final trajectory .xtc obtained cover the

whole
simmulation or I ll have to combine both results?


Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:



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 there was

some
problem (check the .log file itself and stdout/stderr for messages).
Appending is for convenience but there is no functional requirement for
it
(I never append on the fly by personal preference, I just concatenate
later).

-Justin


Thanks in advance.


On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
wrote:

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
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 state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their contents with


gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your
question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete
simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version
5.1.5
-append has been the default option for many years. Again, see the
mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or
send a mail to gmx-users-requ...@gromacs.org.


--

==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

*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#frames Timestep (ps)
Step   27310
Time   27310
Lambda   0
Coords 27310
Velocities   0
Forces   0
Box27310

* gmx check -f traj_comp.xtc*

Checking file traj_comp.xtc
Reading frame   0 time 2720.000
# Atoms  67864
Precision 0.001 (nm)
Last frame 13 time 2850.000


Item#frames Timestep (ps)
Step1410
Time1410
Lambda   0
Coords  1410
Velocities   0
Forces   0
Box 1410


On Fri, May 11, 2018 at 5:12 PM, neelam wafa  wrote:

> 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 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 files but not able to infer a
>>> proper answer.
>>>
>>
>> The file names are contained within the .cpt file, and those are what
>> will be written. You haven't said what your previous command was, but the
>> use of -deffnm makes this much easier:
>>
>> gmx mdrun -deffnm md_0_1 -cpi
>>
>> You will always get clearly named files.
>>
>> If its not appened, will the final trajectory .xtc obtained cover the
>>> whole
>>> simmulation or I ll have to combine both results?
>>>
>>
>> Use gmx check.
>>
>> -Justin
>>
>>
>> Regards
>>>
>>>
>>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:
>>>
>>>
 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 there was
 some
 problem (check the .log file itself and stdout/stderr for messages).
 Appending is for convenience but there is no functional requirement for
 it
 (I never append on the fly by personal preference, I just concatenate
 later).

 -Justin


 Thanks in advance.

> On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
> wrote:
>
> 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
 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 state.cpt. I have got two cpt files
 md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

 Look at the time stamps of the files and inspect their contents with

>>> gmx
>>> check. You will see an obvious difference in what they contain. Also
>>> consult the mdrun help info, which specifically addresses your
>>> question.
>>>
>>> Also I did not get a md_1_0.gro file/ Is is due to incomplete
>>> simmulation?
>>> Yes, because that file is only produced from the last step.
>>>
>>> Also do I need to specify  -append flag or not? I am using version
>>> 5.1.5
>>> -append has been the default option for many years. Again, see the
>>> mdrun
>>> help description.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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 set of files (because -s md_0_1.tpr does not 
write files with names md_0_1.*, only -deffnm does). Your new .log file 
should clearly indicate what time it started from. If it's t=0, then 
your loading from .cpt failed and your run started over. With new file 
names, you shouldn't have lost anything and could try to restart again 
once you identify the source of the problem.


-Justin



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 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 files but not able to infer a
proper answer.


The file names are contained within the .cpt file, and those are what will
be written. You haven't said what your previous command was, but the use of
-deffnm makes this much easier:

gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.

If its not appened, will the final trajectory .xtc obtained cover the whole

simmulation or I ll have to combine both results?


Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:



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 there was

some
problem (check the .log file itself and stdout/stderr for messages).
Appending is for convenience but there is no functional requirement for
it
(I never append on the fly by personal preference, I just concatenate
later).

-Justin


Thanks in advance.


On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
wrote:

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
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 state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their contents with


gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your
question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete
simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version
5.1.5
-append has been the default option for many years. Again, see the
mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--

==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

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 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 files but not able to infer a
>> proper answer.
>>
>
> The file names are contained within the .cpt file, and those are what will
> be written. You haven't said what your previous command was, but the use of
> -deffnm makes this much easier:
>
> gmx mdrun -deffnm md_0_1 -cpi
>
> You will always get clearly named files.
>
> If its not appened, will the final trajectory .xtc obtained cover the whole
>> simmulation or I ll have to combine both results?
>>
>
> Use gmx check.
>
> -Justin
>
>
> Regards
>>
>>
>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:
>>
>>
>>> 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 there was
>>> some
>>> problem (check the .log file itself and stdout/stderr for messages).
>>> Appending is for convenience but there is no functional requirement for
>>> it
>>> (I never append on the fly by personal preference, I just concatenate
>>> later).
>>>
>>> -Justin
>>>
>>>
>>> Thanks in advance.
>>>
 On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
 wrote:

 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
>>> 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 state.cpt. I have got two cpt files
>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>>
>>> Look at the time stamps of the files and inspect their contents with
>>>
>> gmx
>> check. You will see an obvious difference in what they contain. Also
>> consult the mdrun help info, which specifically addresses your
>> question.
>>
>> Also I did not get a md_1_0.gro file/ Is is due to incomplete
>> simmulation?
>> Yes, because that file is only produced from the last step.
>>
>> Also do I need to specify  -append flag or not? I am using version
>> 5.1.5
>> -append has been the default option for many years. Again, see the
>> mdrun
>> help description.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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.
Why has it happened ? I have checked log files but not able to infer a
proper answer.


The file names are contained within the .cpt file, and those are what 
will be written. You haven't said what your previous command was, but 
the use of -deffnm makes this much easier:


gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.


If its not appened, will the final trajectory .xtc obtained cover the whole
simmulation or I ll have to combine both results?


Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:



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 there was some
problem (check the .log file itself and stdout/stderr for messages).
Appending is for convenience but there is no functional requirement for it
(I never append on the fly by personal preference, I just concatenate
later).

-Justin


Thanks in advance.

On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
wrote:

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
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 state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their contents with

gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete
simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version 5.1.5
-append has been the default option for many years. Again, see the mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

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 files but not able to infer a
proper answer.
If its not appened, will the final trajectory .xtc obtained cover the whole
simmulation or I ll have to combine both results?

Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:

>
>
> 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 there was some
> problem (check the .log file itself and stdout/stderr for messages).
> Appending is for convenience but there is no functional requirement for it
> (I never append on the fly by personal preference, I just concatenate
> later).
>
> -Justin
>
>
> Thanks in advance.
>>
>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
>> wrote:
>>
>> 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
> 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 state.cpt. I have got two cpt files
> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>
> Look at the time stamps of the files and inspect their contents with
 gmx
 check. You will see an obvious difference in what they contain. Also
 consult the mdrun help info, which specifically addresses your question.

 Also I did not get a md_1_0.gro file/ Is is due to incomplete
 simmulation?
 Yes, because that file is only produced from the last step.

 Also do I need to specify  -append flag or not? I am using version 5.1.5
 -append has been the default option for many years. Again, see the mdrun
 help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Assistant Professor
 Virginia Tech Department of Biochemistry

 303 Engel Hall
 340 West Campus Dr.
 Blacksburg, VA 24061

 jalem...@vt.edu | (540) 231-3129
 http://www.thelemkullab.com

 ==

 --
 Gromacs Users mailing list

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

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.


>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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 there was 
some problem (check the .log file itself and stdout/stderr for 
messages). Appending is for convenience but there is no functional 
requirement for it (I never append on the fly by personal preference, I 
just concatenate later).


-Justin


Thanks in advance.

On Fri, May 11, 2018 at 12:06 PM, neelam wafa  wrote:


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
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 state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?


Look at the time stamps of the files and inspect their contents with gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version 5.1.5
-append has been the default option for many years. Again, see the mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

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:

> 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
>>> 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 state.cpt. I have got two cpt files
>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>>
>>
>> Look at the time stamps of the files and inspect their contents with gmx
>> check. You will see an obvious difference in what they contain. Also
>> consult the mdrun help info, which specifically addresses your question.
>>
>> Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?
>>>
>>
>> Yes, because that file is only produced from the last step.
>>
>> Also do I need to specify  -append flag or not? I am using version 5.1.5
>>>
>>
>> -append has been the default option for many years. Again, see the mdrun
>> help description.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

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
>> 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 state.cpt. I have got two cpt files
>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>
>
> Look at the time stamps of the files and inspect their contents with gmx
> check. You will see an obvious difference in what they contain. Also
> consult the mdrun help info, which specifically addresses your question.
>
> Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?
>>
>
> Yes, because that file is only produced from the last step.
>
> Also do I need to specify  -append flag or not? I am using version 5.1.5
>>
>
> -append has been the default option for many years. Again, see the mdrun
> help description.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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

but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?


Look at the time stamps of the files and inspect their contents with gmx 
check. You will see an obvious difference in what they contain. Also 
consult the mdrun help info, which specifically addresses your question.



Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?


Yes, because that file is only produced from the last step.


Also do I need to specify  -append flag or not? I am using version 5.1.5


-append has been the default option for many years. Again, see the mdrun 
help description.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.