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

[C.M.Sampson]

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
  00.00.0

   Energies (kJ/mol)
 Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
5.92468e+031.01216e+037.68471e-016.38163e-013.95610e+00
 LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
 8.66770e+03   -2.27543e+035.12418e+046.45763e+042.11278e+07
   Total EnergyTemperature Pressure (bar)
2.11924e+077.81749e+051.08075e+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=  15.0
 2168
1ETH C11   2.735383   2.672010   1.450194  0.2345 -0.1622
0.2097
1ETHH112   0.015804   2.716597   1.460588  0.8528 -0.7984
0.6605
1ETHH123   2.744822   2.565544   1.409227 -2.3812  2.8618
1.8101
"

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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[gmx-users] Issues with energy when running in the microcanonical ensemble

[C.M.Sampson]

Dear all,

I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE
simulations on ethane in 725 TIP3P water molecules.  I used antechamber
to parametrise my ethane.

I have 2 issues;

Firstly the energy conservation of my simulations seems to get worse as
I lower my timestep, here is an example .mdp file that I'm using:


integrator  = md-vv
gen_vel = no
nsteps  = 100
dt  = 0.001
nstlist = 10
rlist   = 1.3
coulombtype = pme
rcoulomb= 1.0
vdw-type= Shift
rvdw= 1.0
tcoupl  = no
pcoupl  = no
nstenergy   = 100

I found a link describing that it could be an issue with the precision
and that Gromacs can be installed with double precision:

http://www.gromacs.org/Documentation/Terminology/Conserving_Energy

but is this the only way to ensure energy conservation?

My second issue is with the calculation of the kinetic energy, I have
2183 atoms in my simulation box which means the kinetic energy should be
(roughly)

0.5 * 3*2183-3(degrees of freedom) * 0.001987204118(kB) * 300(T) *
4.184(conversion from kcal/mol to kJ/mol) = 8163.97

however, when I look in my simulation the kinetic energy Gromacs outputs
is 5498.20 

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
5.95743e+001.96046e+014.71247e-015.73520e-013.92661e+00
LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
5.12842e+03   -3.20604e+04   -2.67111e+03   -2.95726e+045.49820e+03
Total EnergyTemperature Pressure (bar)
   -2.40744e+043.02575e+02   -1.82251e+03

By running in NVE I'm not using a thermostat and can't find any reason
in the manual to scale the kinetic energy.  Is there an a reason I'm
missing as to why my kinetic energy seems lower than it should be?

Best Wishes

Chris







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