[gmx-users] Finishing time donot showing

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 20 20:35:31 CEST 2010 

Hi Bharath,

It means updating the neighbor lists every 10 steps. You might want to
check the manual on those options. Also, you're writing full precision
coordinates and velocities very often, and you're writing coordinates
to the .xtc file as often as to the .trr file, which is redundant
anyhow. You might want to spend a few moments of thought on your
intention with the results, and use that to choose those settings
optimally. There aren't too many purposes for having such a high
resolution for all of the system for a long time. It might well be
sufficient to have nstxout and nstvout set to something corresponding
to every ns, and have the nstxtcout set to something that will yield a
few thousand frames. But it depends on the purpose of course. That's
one of the critical moments in setting up your simulations.

Cheers,

Tsjerk

On Tue, Apr 20, 2010 at 8:22 PM, Bharath.K. Chakravarthi
<bharath.chakravarthi at gmail.com> wrote:
> that means generating a trajectory file for every 10 steps rite
> then i may need  more disk space
>
>
> On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole <x.periole at rug.nl> wrote:
>>
>> On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote:
>>
>> no i did not used -v flag at that command may be thats the mistake
>> thank u Justin
>> On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul <jalemkul at vt.edu>
>> wrote:
>>>
>>>
>>> Bharath.K wrote:
>>>>
>>>> I'm using gromacs-3.3.3 and here is the parameter
>>>>
>>>> ..
>>>> ..
>>>> nstxout             =  500
>>>> nstvout             =  1000
>>>> nstfout             =  0
>>>> nstlist             =  100
>>
>> This might not be the best choice! it is generally kept under 10! It
>> depends on your
>> system/force field though....
>>>>
>>>> nstlog              =  100
>>>> nstenergy           =  10
>>>> nstxtcout           =  500
>>>> ..
>>>> ..
>>>>
>>>>  for writing trajectories in .mdp file and what is check point file and
>>>> -cpi file.cpt ...
>>>> i did not get u.... :(
>>>>
>>>
>>> This is why stating your Gromacs version at the outset is useful.
>>>  Checkpointing was introduced in Gromacs 4.0, so you won't be able to use
>>> it.
>>>
>>> You also have not answered my first question.  What is your mdrun command
>>> line?  Did you use the -v flag?  If not, you will not get any information
>>> about completion time.  There is nothing that the .mdp options or tpbconv
>>> will do for you as far as completion time is concerned.
>>>
>>> -Justin
>>>
>>>> On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole <x.periole at rug.nl>
>>>> wrote:
>>>>
>>>>>
>>>>>>
>>>>>> >tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000
>>>>>> this shows last step before crashing and starts from there until 1000
>>>>>>
>>>>>
>>>>>> then
>>>>>>
>>>>>> >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -
>>>>>> e minim_ener_01.edr
>>>>>>
>>>>>
>>>>> Nothing seem particularly wrong! May be you write your trajectory file
>>>>> too often! Did the original the indicated the same amount of data to be
>>>>> written?
>>>>>
>>>>> which version of gmx you are using? actually using the check point
>>>>> file is relatively easy (-cpi fie.cpt to add to mdrun) and does all
>>>>> the work for you!
>>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole <x.periole at rug.nl>
>>>>>> wrote:
>>>>>>
>>>>>> On Apr 20, 2010, at 9:14 AM, Bharath.K wrote:
>>>>>>
>>>>>> Hello all....
>>>>>> i got a system crash at some steps..
>>>>>> after creating the new .trr file using command tpbconv
>>>>>> trr file with tpbconv? you mean tpr?
>>>>>> and running MDS
>>>>>> what is MDS?
>>>>>>
>>>>>> by mdrun command the approximate finishing time is not showing.....
>>>>>> and also a warning is showing as
>>>>>>
>>>>>> WARNING: this run may generate approximately 4583292 Mb of data....
>>>>>> That is a bit enormous
>>>>>>
>>>>>>
>>>>>> is there any changes that i should do while giving the command and
>>>>>> can i continue with this warning.....
>>>>>> Which exact command did you use?
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Bharath.K
>>>>>> Ph-9535629260
>>>>>> --
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>>>>>>
>>>>>>
>>>>>> --
>>>>>> Bharath.K.Chakravarthi
>>>>>> Ph:9535629260
>>>>>> --
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>>>>>
>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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>>
>>
>>
>> --
>> Bharath.K.Chakravarthi
>> Ph:9535629260
>> --
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>
>
>
> --
> Bharath.K.Chakravarthi
> Ph:9535629260
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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