[gmx-users] Finishing time donot showing
Justin A. Lemkul
jalemkul at vt.edu
Tue Apr 20 20:34:01 CEST 2010
Bharath.K. Chakravarthi wrote:
> that means generating a trajectory file for every 10 steps rite
> then i may need more disk space
>
The nstlist parameter has nothing to do with trajectory output. It is the
frequency with which the neighborlist is updated. Setting this value too high
can (and will!) result in missed short-range interactions and artefacts in the
results. Consult the primary literature for whatever force field you're using
for an appropriate setting (generally 5-10 in conjunction with a 2-fs timestep,
such that the neighborlist is re-generated every 10-20 fs).
-Justin
>
>
> On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole <x.periole at rug.nl
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <http://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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>
>
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> Bharath.K.Chakravarthi
> Ph:9535629260
>
--
========================================
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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