tekle...@ualberta.ca wrote:
Dear Chris and Justin,
I just read the manual and it stated that I need a .trr file if I want
to extend the simulation ( from 5ns -20ns).
My question is:
For the first 5ns I want to use berendsen thermostat and barostat so
that my system will relax faster compared to N-H and P-R. Then I will
switch on to the Nose-Hover and Parrinello-Rahman ( this will give me a
correct description for the kinetic energy information.
Therefore, I need both coordinate and velocity files then ( Gromacs 3.3.3).
nstxout = 50000
nstvout = 50000
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 2000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 2000
xtc-precision = 1000
rather than set the values of nstxout and nstvout , if I set them to
50000, I could get the .trr file. But for my entire analysis I will
depend on the .xtc file.
step 1
after 5ns of my simulation( Both berendsen thermostat and barostat. I
have to use still grompp to generate a new .tpr file by modifying the
.mdp file ( t_ coupling,p_couple and the tinit). Once done this I run
mdrun.
step 2
use the following procedure then after
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr
-extend timetoextend
Am I correct? and also is the output file seems reasonable.
That's certainly a reasonable way to extend a simulation. With 3.3.3, you need
full-precision coordinates and velocities. Is there any reason you want to use
software that is several years old? The upgrades in the 4.0.x series are quite
nice, and make extending simulations far easier, requiring only a checkpoint
file. This (I assume) is why Chris said that the .trr file is becoming obsolete.
I am trying to balance both the disk space issue and what output I need
to continue further.
If you only need the .trr file to continue your simulation, you only need the
very last frame, so there is really no reason to save high-precision coordinates
every few ps for 5 ns. Your .trr file may exceed several GB in size, all for no
reason!
-Justin
Thank you chris and justine.
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
Dear Chris,
Thank you very much!
I am planning to set the output control option like this!
tinit = 0
nstxout = 2000
nstvout = 0
nstfout = 0
nstlog = 2000
nstenergy = 1000
I want to set the velocity and force option to zero and save the
coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By
doing this am I missing anything.
Unless you need full-precision coordinates every few ps, you can use
nstxtcout = 2000 and set nstxout = 0. A .xtc file is substantially
smaller than a .trr file.
-Justin
regards,
Rob
Quoting chris.ne...@utoronto.ca:
Dear Rob:
To answer your question: just set up your run with nsteps for 5 ns,
run mdrun, and then use tpbconv -until. A simpler option is to set
it up to run 20 ns, but use -maxh to limit it to an amount of
runtime that you pre-calculate to be similar to 5 ns of simulation.
HOWEVER:
You almost surely don't need to save this so often: nstxout = 100
(also nstvout, nstfout).
And you may not even need to save this so often: nstxtcout = 100
(also nstenergy).
I had no idea that there was an option nstcheckpoint = 100 as I use
mdrun -cpt 6 to specify a .cpt file every 6 hours, but there is no
need to write a .cpt every 100 steps.
Dear Gromacs users,
I am running an MD simulation but it looks to me that I am running out
of disk space.
This is my .mdp file
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100
nstvout = 100
nstfout = 100
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file
nstxtcout = 100
xtc-precision = 100
nstcheckpoint = 100 ; checkpointing helps you continue
after crashe. This checkpint file is saved every 1ns
Please tell me which files i need to set zero.
I am planning to run my simulation for 20ns but I want it to run every
five nanoseconds until i see an aggregations in my system. So how can
I re-start my simulation every 5ns.
Thank you for your help
rob
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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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========================================
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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