[gmx-users] Larger number of decimal places for coordinates with velocities

C.M.Sampson cms1g11 at soton.ac.uk
Fri Jul 5 17:16:00 CEST 2013

Dear all,

I use Gromacs 4.5.5 with the AMBER ff99SB force field.

I'm working on a method that requires me to run short NVE simulations
one after the other, but randomly generating velocities at the start of
each simulation. i.e. I would run 10 ps, use the final structure with
new random velocities and run another 10 ps.

I had issues with the final potential energy of the previous simulation
not matching the first potential energy of the current simulation, but
managed to fix that by converting the coordinates from the .xtc file to
a .gro file.

My problem is that when I then put the velocities into my new .gro file
the simulation breaks after the first step and the kinetic energy is way
too high:

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
     Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
5.92468e+03    1.01216e+03    7.68471e-01    6.38163e-01    3.95610e+00
     LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
 8.66770e+03   -2.27543e+03    5.12418e+04    6.45763e+04    2.11278e+07
   Total Energy    Temperature Pressure (bar)
    2.11924e+07    7.81749e+05    1.08075e+07

The temperature should be 300K and if I use a .gro file with less
decimal places these same velocities work.

I thought it had to be the way I had formatted my .gro file, but found
the following:

This format is fixed, ie. all columns are in a fixed position.
Optionally (for now only yet with trjconv) you can write gro files with
any number of decimal places, the format will then be n+5 positions with
n decimal places (n+1 for velocities) in stead of 8 with 3 (with 4 for
velocities). Upon reading, the precision will be inferred from the
distance between the decimal points (which will be n+5). Columns contain
the following information (from left to right): 
      * residue number (5 positions, integer)
      * residue name (5 characters)
      * atom name (5 characters)
      * atom number (5 positions, integer)
      * position (in nm, x y z in 3 columns, each 8 positions with 3
        decimal places)
      * velocity (in nm/ps (or km/s), x y z in 3 columns, each 8
        positions with 4 decimal places)

within http://manual.gromacs.org/online/gro.html .

An extract of my .gro file can be seen below:

Generated by trjconv : 2168 system t=  15.00000
    1ETH     C1    1   2.735383   2.672010   1.450194  0.2345 -0.1622
    1ETH    H11    2   0.015804   2.716597   1.460588  0.8528 -0.7984
    1ETH    H12    3   2.744822   2.565544   1.409227 -2.3812  2.8618

I was wondering if there's a way to use a larger number of decimal
places for the coordinates with velocities?

Best Wishes

Chris Sampson

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