On 8/8/18 10:33 AM, ARNAB MUKHERJEE wrote:
Hi,
Thank you very much for your suggestion.
By "nsteps" I meant the # of step interval between which I would record the
velocity. So my simulation run has 10 million steps (200 ns) and I chose
nstvout = 1000.
But I was wondering is it possible to do a mdrun -rerun (changing the .mdp
file), and compute the velocity for the old trajectory (.trr) file, rather
than running a new simulation again?
The -rerun function is for re-evaluating energies of provided
configurations. I don't think it provides any reliable estimate of
velocities.
-Justin
Thanks and Regards,
Arnab
On Wed, Aug 8, 2018 at 4:15 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/7/18 1:47 PM, ARNAB MUKHERJEE wrote:
Dear all,
I have simulated a system of DNA and Protein, and I want to calculate the
velocity of the center of mass of protein as a function of time. So I used
the following command :
gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov
test-vel.xvg -com
I have pasted below the file that it generates :
# GROMACS: gmx traj, VERSION 5.0.6
# Executable: /applic/applications/GROMACS/5.0.6/bin/gmx
# Library dir: /applic/applications/GROMACS/5.0.6/share/gromacs/top
# Command line:
# gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov
test-vel.xvg -com
# gmx is part of G R O M A C S:
#
# Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
#
@ title "Center of mass velocity"
@ xaxis label "Time (ps)"
@ yaxis label "Velocity (nm/ps)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein X"
@ s1 legend "Protein Y"
@ s2 legend "Protein Z"
"test-vel.xvg" 24L, 731C 24,1
Bot
So it doesn't have the velocities. Is it due to the fact that in my .mdp
file, I had set nstvout = 0 ? I have pasted below the initial part of my
.mdp file
title = NVT equilibration with position restraint on all solute
(topology modified)
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 1 * 500000 = 500 ps
;nsteps = 5000
dt = 0.02 ; 1 fs
; Output control
nstxout = 0 ; save coordinates every 10 ps
nstvout = 0 ; save velocities every 10 ps
nstcalcenergy = 50
nstenergy = 1000 ; save energies every 1 ps
nstxtcout = 2500
;nstxout-compressed = 5000 ; save compressed coordinates every 1.0 ps
; nstxout-compressed replaces nstxtcout
;compressed-x-grps = System ; replaces xtc-grps
nstlog = 1000 ; update log file every 1 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds)
constrained
;lincs_iter = 2 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
Is there a way I can still compute the velocities, or do I need to run the
simulation again, putting nstvout = nsteps ?
Yes, you need a non-zero value for nstvout, but you shouldn't set it to
the same value as nsteps, because then you'll only get one frame. You need
some sensible output frequency that allows you to collect relevant
statistics of the quantity of interest.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
