[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

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Thu May 18 18:44:10 CEST 2017


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  mass    charge  ptype         sigma     epsilon 
CR         6   12.0110   0.0        A      0.387541    0.230120  
CO2M       6   12.0110   0.0        A      0.356359    0.292880   
HCMM       1    1.0079   0.0        A      0.235197    0.092048  
HNRP       1    1.0079   0.0        A      0.040001    0.192464  
NRP        7   14.0067   0.0        A      0.329632    0.836800  
O2CM       8   15.9994   0.0        A      0.302905    0.502080

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: 18 May 2017 16:33
To: gmx-users at 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 
> <mark.j.abraham at gmail.com>
> 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_p130085bt at 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     3530.00000        0.00000
>>>
>>>    Energies (kJ/mol)
>>>        G96Angle    Proper Dih.  Improper Dih.          LJ-14
>>> Coulomb-14
>>>     6.73096e+03    3.13198e+03    2.15931e+03    1.31375e+03
>>> 4.51549e+04
>>>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>> Potential
>>>     3.66659e+05   -7.80170e+03   -2.71529e+06    4.12416e+03
>>> -2.29382e+06
>>>     Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure
>>> (bar)
>>>     4.12474e+05   -1.88135e+06    3.00209e+02   -7.62778e+01
>>> 2.10104e+01
>>>    Constr. rmsd
>>>     2.37431e-05
>>> ------------------------------------------------------------
>>> -------------------------------------
>>> md.log (final)
>>> ----------
>>>         Step           Time         Lambda
>>>         4000000     8000.00000        0.00000
>>>
>>> Writing checkpoint, step 4000000 at Thu May 18 13:55:01 2017
>>>
>>>
>>>    Energies (kJ/mol)
>>>        G96Angle    Proper Dih.  Improper Dih.          LJ-14
>>> Coulomb-14
>>>     6.44959e+03    3.18212e+03    2.06343e+03    1.53953e+03
>>> 4.49878e+04
>>>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>> Potential
>>>     3.66131e+05   -7.78489e+03   -2.71259e+06    4.78708e+03
>>> -2.29124e+06
>>>     Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure
>>> (bar)
>>>     4.13852e+05   -1.87738e+06    3.01212e+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:   312346.797    39374.380      793.3
>>>                          10h56:14
>>>                  (ns/day)    (hour/ns)
>>> Performance:        9.967        2.408
>>> 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 
>>> re-starting a stopped simulation is not working.
>>>
>>> Is it any modification in 're-start' command is required?
>>>
>>> Regards,
>>> Adarsh V. K.
>>>
>>>

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

==================================================
--
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-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list