[gmx-users] Larger number of decimal places for coordinates with velocities
mark.j.abraham at gmail.com
Fri Jul 5 21:37:08 CEST 2013
On Fri, Jul 5, 2013 at 5:16 PM, C.M.Sampson <cms1g11 at soton.ac.uk> wrote:
> 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.
Seems like you're not using the unconstrained-start .mdp option correctly.
> 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.
The .gro format is fixed-width, and that's life. The above results are
an immediate consequence of breaking the rules.
> 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?
The .g96 file format has many digits and text representation. Use
mdrun -c file.g96 with otherwise normal inputs to get an example to
> Best Wishes
> Chris Sampson
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