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.peri...@rug.nl
<mailto:x.peri...@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
<jalem...@vt.edu <mailto: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 <mailto: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 <mailto: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
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the
list. Use thewww
interface or send it to
gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the
list. Use thewww
interface or send it to
gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
Bharath.K.Chakravarthi
Ph:9535629260
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the
list. Use the
www interface or send it to
gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Bharath.K.Chakravarthi
Ph:9535629260
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
