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.
I am trying to balance both the disk space issue and what output I
need to continue further.
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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