[gmx-users] gmx mdrun -rerun issue

[Benson Muite]

Hi Andreas,

I tried it on my laptop:

gmx mdrun -rerun old_PROD.trr -deffnm new_PROD

and got the following output:

  gmx mdrun -rerun old_PROD.trr -deffnm new_PROD
                       :-) GROMACS - gmx mdrun, 2018.3 (-:

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GROMACS:      gmx mdrun, version 2018.3
Executable: /home/benson/Projects/GromacsTest/gromacsinstall/bin/gmx
Data prefix:  /home/benson/Projects/GromacsTest/gromacsinstall
Working dir: /home/benson/Projects/GromacsTest/small_rerun_example
Command line:
   gmx mdrun -rerun old_PROD.trr -deffnm new_PROD


Back Off! I just backed up new_PROD.log to ./#new_PROD.log.1#
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
X server found. dri2 connection failed!
Reading file new_PROD.tpr, VERSION 2016.1 (single precision)
Note: file tpx version 110, software tpx version 112
Changing nstlist from 10 to 100, rlist from 1.2 to 1.201

Using 1 MPI thread
Using 4 OpenMP threads


Back Off! I just backed up new_PROD.trr to ./#new_PROD.trr.1#

Back Off! I just backed up new_PROD.edr to ./#new_PROD.edr.1#
starting md rerun 'Ethanol_Ethanol', reading coordinates from input 
trajectory 'old_PROD.trr'

trr version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
WARNING: Some frames do not contain velocities.
          Ekin, temperature and pressure are incorrect,
          the virial will be incorrect when constraints are present.

Reading frame       1 time   10.000
step -1: resetting all time and cycle counters
Last frame        200 time 2000.000

NOTE: 39 % of the run time was spent in pair search,
       you might want to increase nstlist (this has no effect on accuracy)

                Core t (s)   Wall t (s)        (%)
        Time:        5.795        1.449      400.0
                  (ns/day)    (hour/ns)
Performance:        0.030      804.864

GROMACS reminds you: "Molecular biology is essentially the practice of 
biochemistry without a license." (Edwin Chargaff)


Perhaps try a newer version of GROMACS? Rather than using a provided 
module, you can install it in your home directory on your cluster.

Regards,

Benson

On 10/11/18 1:51 PM, Andreas Mecklenfeld wrote:
> Dear Benson,
>
> thanks for the offer. I've used gmx traj to generate a smaller *.trr 
> file, though the occuring issue seems unaffected.
> I've uploaded my files to http://ge.tt/1HNpO8s2
>
>
> Kind regards,
> Andreas
>
>
>
> Am 09.10.2018 um 10:48 schrieb Benson Muite:
>> Current version 2018.3 seems to have re-run feature:
>>
>> http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html 
>>
>>
>> Is your input data reasonable? Might a small version be available where
>> one could try this in 2018.3 to see if the same error is obtained?
>>
>> Benson
>>
>> On 10/9/18 11:40 AM, Andreas Mecklenfeld wrote:
>>> Hey,
>>>
>>> thanks for the quick response. Unfortunately, there isn't (at least
>>> not in the short-term). Which one would be suitable though?
>>>
>>> Best regards,
>>> Andreas
>>>
>>>
>>>
>>> Am 09.10.2018 um 10:31 schrieb Benson Muite:
>>>> Hi,
>>>>
>>>> Is it possible to use a newer version of Gromacs?
>>>>
>>>> Benson
>>>>
>>>> On 10/9/18 11:15 AM, Andreas Mecklenfeld wrote:
>>>>> Dear Gromacs users,
>>>>>
>>>>>
>>>>> I've a question regarding the rerun option of the mdrun command in
>>>>> Gromacs 2016.1. It seems as if the calculation is repeatedly 
>>>>> performed
>>>>> for the last frame (until killed by the work station). The output is
>>>>>
>>>>> "Last frame    1000 time 2000.000
>>>>>
>>>>> WARNING: Incomplete header: nr 1001 time 2000"
>>>>>
>>>>>
>>>>> My goal is to alter the .top-file (new) and calculate energies with
>>>>> previously recorded coordinates (old): "gmx grompp -f old_PROD.mdp -c
>>>>> old_PROD.gro -p new_topol.top -o new_PROD.tpr"
>>>>>
>>>>> The mdrun looks like "gmx mdrun -rerun old_PROD.trr -deffnm new_PROD"
>>>>>
>>>>>
>>>>> Is there a way to fix this?
>>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Andreas
>>>>>
>>>>>