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 <jalem...@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.peri...@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.peri...@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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--
========================================
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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Ph:9535629260
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