Dear Justin,
The reply is below:
I am doing a simulation of a carbon nanotube (CNT) inside water. First I am
going to describe my problem and then give info about my simulation setup
(initial conditions, parameters, etc.).
My problem is as follows:
(1) I am doing a *.gro file of a *.pdb of a (16,16) CNT, without using
pdb2gmx, that is with my own code. I also add manually velocity columns (vx,
vy, vz) = (0, 0, 0) to the *.gro file. It works properly, since VMD and
various gromacs commands can process the *.gro file.
(2) Then, I use editconf in order to center the nanotube and set up a
rectangular box. There, when I give a finite velocity (just to check) to
every carbon (C) atom in CNT , such as (vx, vy, vz) = (0.0001, 0.0001,
0.0001) for every C, then editconf preserves the velocity info and includen
in the output *.gro file. In fact I should fix the position of the nanotube.
But when (vx, vy, vz) = (0, 0, 0), then it says "cannot find velocity
information" or something like that and ignores the velocity columns.
Telling us "or something like that" does not make it easy for us to help you.
What was your exact command line input, and what was the exact message? Likely
it stems from using velocities of 0, 0, 0. The .gro format is fixed:
http://www.gromacs.org/documentation/reference/online/gro.html
My command line input is:
editconf -f CNT1616_L50_1.gro -o CNT1616_50_wbox.gro -box 8.0 6.0 6.0 -c
The output is:
...
Read 1280 atoms
Volume: 125 nm^3, corresponds to roughly 56200 electrons
No velocities found
system size : 4.920 2.170 2.170 (nm)
center : 0.000 -0.000 0.000 (nm)
box vectors : 5.000 5.000 5.000 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 125.00 (nm^3)
shift : 4.000 3.000 3.000 (nm)
new center : 4.000 3.000 3.000 (nm)
new box vectors : 8.000 6.000 6.000 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 288.00 (nm^3)
...
That is, the message is "No velocities found". Note that editconf
succeeds, so "No velocities found" is not an error.
To be more clear (as you suggested) :
My gro file is as follows:
Carbon Nanotube
1280
1 CNT C1 1 -2.460 0.603 0.902 0.000 0.000 0.000
1 CNT C2 2 -2.337 0.661 0.861 0.000 0.000 0.000
1 CNT C3 3 -2.460 0.902 0.603 0.000 0.000 0.000
1 CNT C4 4 -2.337 0.940 0.542 0.000 0.000 0.000
1 CNT C5 5 -2.460 1.064 0.212 0.000 0.000 0.000
1 CNT C6 6 -2.337 1.076 0.142 0.000 0.000 0.000
1 CNT C7 7 -2.460 1.064 -0.212 0.000 0.000 0.000
1 CNT C8 8 -2.337 1.048 -0.281 0.000 0.000 0.000
1 CNT C9 9 -2.460 0.902 -0.603 0.000 0.000 0.000
1 CNT C10 10 -2.337 0.861 -0.661 0.000 0.000 0.000
...
There is no problem with gro format. This is why I wrote " It works
properly, since VMD and various gromacs commands can process the *.gro
file" in my previous message.
(3) So, after that, when I use genbox in order to fill the box with water,
than all the velocity information disappears, no matter whether the initial
velocity for C atoms are finite or simply 0. The gro file includes the
coordinates of both CNT and H2O molecules, but there is no velocity info!
See genbox -h for why this happens.
(4) Then I run grompp with my output *.gro file, *.top (topology) file and
*.mdp file which I will describe the settings below, in order to produce a
*.tpr file. When I read the resulting *.tpr file with gmxdump, again there
are just coordinates, no velocity columns.
Probably because you have gen_vel = no, and there are no velocities in the input
file (see above).
Then how does the simulation calculate the equations of motion?
As it is obvious from physics and from the gromacs manual, the initial
velocities should be set to zero by default by the program.
(5) I do an energy minimisation step, I check the output (both the *.trr file
and *.gro file) again there is no velocity info.
As there shouldn't be, for an energy minimization.
(6)After that, again I modify my *.mdp file in order to do MD, I run grompp
just as before, than mdrun, and there is no velocity info both in *.trr and
*.xtc files, even if nvout=positive integer and gen_vel=yes (when it is set
to be"no", then again there should be velocity info in the following time
steps). I also tried to put to input *.gro file velocity columns by hand, but
it didn't work.
What didn't work? Again, be more specific. What were your commands, and what
output did you receive? Your .mdp file looks fine with respect to velocity
generation and output parameters. Does the simulation run to completion?
"It didn't work" == "there is no velocity info both in *.trr and *.xtc
files, even if nvout=positive integer and gen_vel=yes"
The simulation was complete, and it was pretty succesful, I was able to
reproduce some results in the literature. But I still need the velocity
info.
P.S. :Here is a part of my mdp file for md:
cpp = /usr/bin/cpp ; Preprocessor
define =-DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator = md ; Algorithm (steep = steepest descent
minimization)
dt = 0.002 ; time step
nsteps = 2500000 ; 5 ns
nstenergy = 1000 ; Write energies to disk every nstenergy steps
nstxout = 5000 ; collect data every 10 ps
nstvout = 5000
nstxtcout = 1000 ; Write coordinates to disk every nstxtcout
steps
xtc_grps = CNT SOL ; Which coordinate group(s) to write to disk
energygrps = CNT SOL ; Which energy group(s) to write to disk
energygrp_excl = CNT CNT
gen-vel = no
gen-temp = 300
gen-seed = 173529
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
compressibility = 4.5E-5
nstlist = 15 ; Frequency to update the neighbor list and
long range forces
ns_type = grid ; Method to determine neighbor list (simple,
grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range
forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
fourierspacing = 0.12 ; FFT grid spacing
pme_order = 4
optimize_fft = yes
freezegrps = CNT
freezedim = Y Y Y
acc_grps = SOL
accelerate = 0.002 0 0 ;
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
ref_p = 1.0 1.0
tau_p = 0.5
tcoupl = nose-hoover
tc_grps = CNT SOL
ref_t = 300 300
tau_t = 0.2 0.2 neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range
forces)
coulombtype
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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