[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)
Nadir Kaplan
cikaplan at ku.edu.tr
Thu May 22 13:02:53 CEST 2008
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
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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