Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

2017-05-18 Thread Justin Lemkul 



On 5/18/17 12:44 PM, Pandya, Akash wrote:

I've read the errors documentation. The atomtypes directive does appear before 
any molecule types directive in my itp file. I tried changing the order it 
still comes up as an error



Table 5.4 in the PDF manual has the order that directives must appear.  Your 
[atomtypes] must be out of order with respect to some other directive.


-Justin


[ atomtypes ]
; name atomnum  masscharge  ptype sigma epsilon
CR 6   12.0110   0.0A  0.3875410.230120
CO2M   6   12.0110   0.0A  0.3563590.292880
HCMM   11.0079   0.0A  0.2351970.092048
HNRP   11.0079   0.0A  0.0400010.192464
NRP7   14.0067   0.0A  0.3296320.836800
O2CM   8   15.9994   0.0A  0.3029050.502080

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 May 2017 16:33
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Can you please tell me the exact command? Re: Restart 
a stopped simulation after a power failure? : Not working in Gromacs 5.1.4



On 5/18/17 11:30 AM, Adarsh V. K. wrote:

Dear Dr. Mark,

Thank you for the prompt reply. I have been struggling with the issue
for couple month time. Would you please advise me how to use  "
-deffnm " flag in commands?

# gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm

Will the above command will successful restart a stopped simulation
and append?, If no could you please type the exact command I
should use to solve the issue.



The -deffnm command sets the default file prefix for all output files.  So if 
you issue:

gmx mdrun -deffnm md_0_1

You will get all files name md_0_1.* as output.

If you extend the simulation (e.g. gmx convert-tpr -extend) and keep the same 
file name (e.g. md_0_1.tpr now just contains more steps)

gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt

That's all there is to it.

-Justin


Sincerely,

Adarsh V. K.
Research Scholar (PhD)
National Institute of Technology, Calicut ( NIT C ) Kerala state,
India

--
 On Thu, May 18, 2017 at 7:13 PM, Mark Abraham

wrote:


Hi,

Some of your commands and outputs are inconsistent. You can't get
md_0_1.log without e.g. using -deffnm, and you'll only get md.log if
you don't use deffnm. But if you change that when trying to do your
continuation, mdrun won't know how to append because you haven't told
it that the old name. Be consistent. Your whole trajectory is present
in all your output files, but you're going to have to concatenate
them yourself, e.g. with gmx trjcat since you didn't tell mdrun a
consistent name for the files.

GROMACS 2016 likely refuses to do your continuation, precisely so
that you are prompted to say what you actually want, rather than
mdrun trying to be clever and getting it wrong.

Mark

On Thu, May 18, 2017 at 11:03 AM Adarsh V. K.

wrote:


Dear gmx users,

I use Gromacs 5.1.4 for protein ligand simulation. How can I restart
a stopped simulation after a power failure? (used 8 processor cores
+ Graphics card GTX 780Ti).

I have attached the log file along with this mail.

It appeared that no details appended after restarting simulation
(after power failure at 3.5 ns), Even Though the 'terminal' Ubuntu
16.04 shows that the simulation successfully restarted from 3.5 ns
(used 8 processor cores + Graphics card GTX 780Ti) and completed the
entire 8 ns simulation...!!. Frames...350 -> 3500 ps (not appended
the log file after the restart from 3500ps to 8000ps).

I used the command (gromacs 5.1.4),
  # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v

I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append



md_0_1.log : (final)
-
Step   Time Lambda
1765000 3530.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14
Coulomb-14
6.73096e+033.13198e+032.15931e+031.31375e+03
4.51549e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
Potential
3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
-2.29382e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
(bar)
4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
2.10104e+01
   Constr. rmsd
2.37431e-05

-
md.log (final)
--
Step   Time Lambda
400 8000.00.0

Writing checkpoint, step 400 at Thu May 18 13:55:01 2017


   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

2017-05-18 Thread Pandya, Akash 
I've read the errors documentation. The atomtypes directive does appear before 
any molecule types directive in my itp file. I tried changing the order it 
still comes up as an error

[ atomtypes ] 
; name atomnum  masscharge  ptype sigma epsilon 
CR 6   12.0110   0.0A  0.3875410.230120  
CO2M   6   12.0110   0.0A  0.3563590.292880   
HCMM   11.0079   0.0A  0.2351970.092048  
HNRP   11.0079   0.0A  0.0400010.192464  
NRP7   14.0067   0.0A  0.3296320.836800  
O2CM   8   15.9994   0.0A  0.3029050.502080

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 May 2017 16:33
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Can you please tell me the exact command? Re: Restart 
a stopped simulation after a power failure? : Not working in Gromacs 5.1.4



On 5/18/17 11:30 AM, Adarsh V. K. wrote:
> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue 
> for couple month time. Would you please advise me how to use  " 
> -deffnm " flag in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation 
> and append?, If no could you please type the exact command I 
> should use to solve the issue.
>

The -deffnm command sets the default file prefix for all output files.  So if 
you issue:

gmx mdrun -deffnm md_0_1

You will get all files name md_0_1.* as output.

If you extend the simulation (e.g. gmx convert-tpr -extend) and keep the same 
file name (e.g. md_0_1.tpr now just contains more steps)

gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt

That's all there is to it.

-Justin

> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C ) Kerala state, 
> India
>
> --
>  On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> 
> wrote:
>
>> Hi,
>>
>> Some of your commands and outputs are inconsistent. You can't get 
>> md_0_1.log without e.g. using -deffnm, and you'll only get md.log if 
>> you don't use deffnm. But if you change that when trying to do your 
>> continuation, mdrun won't know how to append because you haven't told 
>> it that the old name. Be consistent. Your whole trajectory is present 
>> in all your output files, but you're going to have to concatenate 
>> them yourself, e.g. with gmx trjcat since you didn't tell mdrun a 
>> consistent name for the files.
>>
>> GROMACS 2016 likely refuses to do your continuation, precisely so 
>> that you are prompted to say what you actually want, rather than 
>> mdrun trying to be clever and getting it wrong.
>>
>> Mark
>>
>> On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
>> 
>> wrote:
>>
>>> Dear gmx users,
>>>
>>> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart 
>>> a stopped simulation after a power failure? (used 8 processor cores 
>>> + Graphics card GTX 780Ti).
>>>
>>> I have attached the log file along with this mail.
>>>
>>> It appeared that no details appended after restarting simulation 
>>> (after power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 
>>> 16.04 shows that the simulation successfully restarted from 3.5 ns 
>>> (used 8 processor cores + Graphics card GTX 780Ti) and completed the 
>>> entire 8 ns simulation...!!. Frames...350 -> 3500 ps (not appended 
>>> the log file after the restart from 3500ps to 8000ps).
>>>
>>> I used the command (gromacs 5.1.4),
>>>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>>>
>>> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
>>>
>>> 
>>> 
>>> md_0_1.log : (final)
>>> -
>>> Step   Time Lambda
>>> 1765000 3530.00.0
>>>
>>>Energies (kJ/mol)
>>>G96AngleProper Dih.  Improper Dih.  LJ-14
>>> Coulomb-14
>>> 6.73096e+033.13198e+032.15931e+031.31375e+03
>>> 4.51549e+04
>>> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>> Potential
>>> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
>>> -2.29382e+06
>>> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>>> (bar)
>>> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
>>> 2.10104e+01
>>>Constr. rmsd
>>> 2.37431e-05
>>> 
>>> -
>>> md.log (final)
>>> --
>>> Step   Time Lambda
>>> 400 8000.00.0
>>>
>>> Writing checkpoint, step

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

2017-05-18 Thread Justin Lemkul 



On 5/18/17 11:30 AM, Adarsh V. K. wrote:

Dear Dr. Mark,

Thank you for the prompt reply. I have been struggling with the issue for
couple month time. Would you please advise me how to use  " -deffnm " flag
in commands?

# gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm

Will the above command will successful restart a stopped simulation and
append?, If no could you please type the exact command I should use to
solve the issue.



The -deffnm command sets the default file prefix for all output files.  So if 
you issue:


gmx mdrun -deffnm md_0_1

You will get all files name md_0_1.* as output.

If you extend the simulation (e.g. gmx convert-tpr -extend) and keep the same 
file name (e.g. md_0_1.tpr now just contains more steps)


gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt

That's all there is to it.

-Justin


Sincerely,

Adarsh V. K.
Research Scholar (PhD)
National Institute of Technology, Calicut ( NIT C )
Kerala state, India

--
On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
wrote:


Hi,

Some of your commands and outputs are inconsistent. You can't get
md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
don't use deffnm. But if you change that when trying to do your
continuation, mdrun won't know how to append because you haven't told it
that the old name. Be consistent. Your whole trajectory is present in all
your output files, but you're going to have to concatenate them yourself,
e.g. with gmx trjcat since you didn't tell mdrun a consistent name for the
files.

GROMACS 2016 likely refuses to do your continuation, precisely so that you
are prompted to say what you actually want, rather than mdrun trying to be
clever and getting it wrong.

Mark

On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
wrote:


Dear gmx users,

I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
stopped simulation after a power failure? (used 8 processor cores +
Graphics card GTX 780Ti).

I have attached the log file along with this mail.

It appeared that no details appended after restarting simulation (after
power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
that the simulation successfully restarted from 3.5 ns (used 8 processor
cores + Graphics card GTX 780Ti) and completed the entire 8 ns
simulation...!!. Frames...350 -> 3500 ps (not appended the log file after
the restart from 3500ps to 8000ps).

I used the command (gromacs 5.1.4),
  # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v

I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append



md_0_1.log : (final)
-
Step   Time Lambda
1765000 3530.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14
Coulomb-14
6.73096e+033.13198e+032.15931e+031.31375e+03
4.51549e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
Potential
3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
-2.29382e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
(bar)
4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
2.10104e+01
   Constr. rmsd
2.37431e-05

-
md.log (final)
--
Step   Time Lambda
400 8000.00.0

Writing checkpoint, step 400 at Thu May 18 13:55:01 2017


   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14
Coulomb-14
6.44959e+033.18212e+032.06343e+031.53953e+03
4.49878e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
Potential
3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
-2.29124e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
(bar)
4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+01
5.34060e+01
   Constr. rmsd
2.33151e-05
-
Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
For optimal performance this ratio should be close to 1!

   Core t (s)   Wall t (s)(%)
   Time:   312346.79739374.380  793.3
 10h56:14
 (ns/day)(hour/ns)
Performance:9.9672.408
Finished mdrun on rank 0 Thu May 18 13:55:02 2017


---
But while using the command it shows only 3.5 ns of simulation. How to
solve this problem

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
compact

Select 0 ("System")

-

Later I repeated the whole 8 ns

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

2017-05-18 Thread Anshul Lahariya 
Hlw

Plzz use

gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt

On 18 May 2017 9:01 p.m., "Adarsh V. K." 
wrote:

> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue for
> couple month time. Would you please advise me how to use  " -deffnm " flag
> in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation and
> append?, If no could you please type the exact command I should use to
> solve the issue.
>
> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C )
> Kerala state, India
>
> --
> On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Some of your commands and outputs are inconsistent. You can't get
> > md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> > don't use deffnm. But if you change that when trying to do your
> > continuation, mdrun won't know how to append because you haven't told it
> > that the old name. Be consistent. Your whole trajectory is present in all
> > your output files, but you're going to have to concatenate them yourself,
> > e.g. with gmx trjcat since you didn't tell mdrun a consistent name for
> the
> > files.
> >
> > GROMACS 2016 likely refuses to do your continuation, precisely so that
> you
> > are prompted to say what you actually want, rather than mdrun trying to
> be
> > clever and getting it wrong.
> >
> > Mark
> >
> > On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. <
> adarsh_p13008...@nitc.ac.in>
> > wrote:
> >
> >> Dear gmx users,
> >>
> >> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> >> stopped simulation after a power failure? (used 8 processor cores +
> >> Graphics card GTX 780Ti).
> >>
> >> I have attached the log file along with this mail.
> >>
> >> It appeared that no details appended after restarting simulation (after
> >> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
> >> that the simulation successfully restarted from 3.5 ns (used 8 processor
> >> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
> >> simulation...!!. Frames...350 -> 3500 ps (not appended the log file
> after
> >> the restart from 3500ps to 8000ps).
> >>
> >> I used the command (gromacs 5.1.4),
> >>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
> >>
> >> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
> >>
> >> 
> >> 
> >> md_0_1.log : (final)
> >> -
> >> Step   Time Lambda
> >> 1765000 3530.00.0
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.73096e+033.13198e+032.15931e+031.31375e+03
> >> 4.51549e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
> >> -2.29382e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
> >> 2.10104e+01
> >>Constr. rmsd
> >> 2.37431e-05
> >> 
> >> -
> >> md.log (final)
> >> --
> >> Step   Time Lambda
> >> 400 8000.00.0
> >>
> >> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
> >>
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.44959e+033.18212e+032.06343e+031.53953e+03
> >> 4.49878e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
> >> -2.29124e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+01
> >> 5.34060e+01
> >>Constr. rmsd
> >> 2.33151e-05
> >> -
> >> Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
> >> For optimal performance this ratio should be close to 1!
> >>
> >>Core t (s)   Wall t (s)(%)
> >>Time:   312346.79739374.380  793.3
> >>  10h56:14
> >>  (ns/day)(hour/ns)
> >> Performance:9.9672.408
> >> Finished mdrun on rank 0 Thu May 18 13:55:02 2017
> >>
> >> 
> >> ---
> >> But while using the command it shows only 3.5 ns of simulation. How to
> >> solve this problem
> >>
> >>

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

2017-05-18 Thread Mark Abraham 
Hi,

Use

gmx mdrun
gmx mdrun -cpi

so that by default you get appending and the filenames haven't changed.
Later, when you're comfortable, try

gmx mdrun -deffnm whatever
gmx mdrun -deffnm whatever -cpi

but really there's very few cases where deffnm is actually useful. You have
a directory name for organizing your work - do only one simulation in it
and avoid problems from trying to name each file descriptively.

Your problems likely stem from trying to do

gmx mdrun -deffnm whatever
gmx mdrun -s whatever -cpi

but it's hard to guess what you've done from partial reports. If so, you
can do it better by doing

gmx mdrun -deffnm whatever -cpi

Now, you probably need to do

gmx trjcat -f whatever traj -o combined

to get all your output into one file

Hope this helps!

Mark

On Thu, May 18, 2017 at 5:31 PM Adarsh V. K. 
wrote:

> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue for
> couple month time. Would you please advise me how to use  " -deffnm " flag
> in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation and
> append?, If no could you please type the exact command I should use to
> solve the issue.
>
> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C )
> Kerala state, India
>
> --
> On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Some of your commands and outputs are inconsistent. You can't get
> > md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> > don't use deffnm. But if you change that when trying to do your
> > continuation, mdrun won't know how to append because you haven't told it
> > that the old name. Be consistent. Your whole trajectory is present in all
> > your output files, but you're going to have to concatenate them yourself,
> > e.g. with gmx trjcat since you didn't tell mdrun a consistent name for
> the
> > files.
> >
> > GROMACS 2016 likely refuses to do your continuation, precisely so that
> you
> > are prompted to say what you actually want, rather than mdrun trying to
> be
> > clever and getting it wrong.
> >
> > Mark
> >
> > On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. <
> adarsh_p13008...@nitc.ac.in>
> > wrote:
> >
> >> Dear gmx users,
> >>
> >> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> >> stopped simulation after a power failure? (used 8 processor cores +
> >> Graphics card GTX 780Ti).
> >>
> >> I have attached the log file along with this mail.
> >>
> >> It appeared that no details appended after restarting simulation (after
> >> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
> >> that the simulation successfully restarted from 3.5 ns (used 8 processor
> >> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
> >> simulation...!!. Frames...350 -> 3500 ps (not appended the log file
> after
> >> the restart from 3500ps to 8000ps).
> >>
> >> I used the command (gromacs 5.1.4),
> >>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
> >>
> >> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
> >>
> >> 
> >> 
> >> md_0_1.log : (final)
> >> -
> >> Step   Time Lambda
> >> 1765000 3530.00.0
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.73096e+033.13198e+032.15931e+031.31375e+03
> >> 4.51549e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
> >> -2.29382e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
> >> 2.10104e+01
> >>Constr. rmsd
> >> 2.37431e-05
> >> 
> >> -
> >> md.log (final)
> >> --
> >> Step   Time Lambda
> >> 400 8000.00.0
> >>
> >> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
> >>
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.44959e+033.18212e+032.06343e+031.53953e+03
> >> 4.49878e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
> >> -2.29124e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.13852e+05   -1.87738e+063.01212e+02

[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

2017-05-18 Thread Adarsh V. K. 
Dear Dr. Mark,

Thank you for the prompt reply. I have been struggling with the issue for
couple month time. Would you please advise me how to use  " -deffnm " flag
in commands?

# gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm

Will the above command will successful restart a stopped simulation and
append?, If no could you please type the exact command I should use to
solve the issue.

Sincerely,

Adarsh V. K.
Research Scholar (PhD)
National Institute of Technology, Calicut ( NIT C )
Kerala state, India

--
On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
wrote:

> Hi,
>
> Some of your commands and outputs are inconsistent. You can't get
> md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> don't use deffnm. But if you change that when trying to do your
> continuation, mdrun won't know how to append because you haven't told it
> that the old name. Be consistent. Your whole trajectory is present in all
> your output files, but you're going to have to concatenate them yourself,
> e.g. with gmx trjcat since you didn't tell mdrun a consistent name for the
> files.
>
> GROMACS 2016 likely refuses to do your continuation, precisely so that you
> are prompted to say what you actually want, rather than mdrun trying to be
> clever and getting it wrong.
>
> Mark
>
> On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
> wrote:
>
>> Dear gmx users,
>>
>> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
>> stopped simulation after a power failure? (used 8 processor cores +
>> Graphics card GTX 780Ti).
>>
>> I have attached the log file along with this mail.
>>
>> It appeared that no details appended after restarting simulation (after
>> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
>> that the simulation successfully restarted from 3.5 ns (used 8 processor
>> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
>> simulation...!!. Frames...350 -> 3500 ps (not appended the log file after
>> the restart from 3500ps to 8000ps).
>>
>> I used the command (gromacs 5.1.4),
>>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>>
>> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
>>
>> 
>> 
>> md_0_1.log : (final)
>> -
>> Step   Time Lambda
>> 1765000 3530.00.0
>>
>>Energies (kJ/mol)
>>G96AngleProper Dih.  Improper Dih.  LJ-14
>> Coulomb-14
>> 6.73096e+033.13198e+032.15931e+031.31375e+03
>> 4.51549e+04
>> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>> Potential
>> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
>> -2.29382e+06
>> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>> (bar)
>> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
>> 2.10104e+01
>>Constr. rmsd
>> 2.37431e-05
>> 
>> -
>> md.log (final)
>> --
>> Step   Time Lambda
>> 400 8000.00.0
>>
>> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
>>
>>
>>Energies (kJ/mol)
>>G96AngleProper Dih.  Improper Dih.  LJ-14
>> Coulomb-14
>> 6.44959e+033.18212e+032.06343e+031.53953e+03
>> 4.49878e+04
>> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>> Potential
>> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
>> -2.29124e+06
>> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>> (bar)
>> 4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+01
>> 5.34060e+01
>>Constr. rmsd
>> 2.33151e-05
>> -
>> Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
>> For optimal performance this ratio should be close to 1!
>>
>>Core t (s)   Wall t (s)(%)
>>Time:   312346.79739374.380  793.3
>>  10h56:14
>>  (ns/day)(hour/ns)
>> Performance:9.9672.408
>> Finished mdrun on rank 0 Thu May 18 13:55:02 2017
>>
>> 
>> ---
>> But while using the command it shows only 3.5 ns of simulation. How to
>> solve this problem
>>
>> gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
>> compact
>>
>> Select 0 ("System")
>> 
>> -
>>
>> Later I repeated the whole 8 ns simulation from beginning It
>> completed with out any issues.
>>
>> Can any body tell me what happens during the power failure and why
>>