[gmx-users] Finishing time donot showing
Bharath.K. Chakravarthi
bharath.chakravarthi at gmail.com
Tue Apr 20 20:22:45 CEST 2010
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
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
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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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