[gmx-users] Simulating crystalls

karamyog singh karamyog.singh at gmail.com
Fri May 26 10:22:22 CEST 2006

Does this give any clue. It shows large PE, KE and temp. Could that be a
reason? More information required?

However, I have chenged my system a bit. My conf.gro file has just 2 atoms.
one at the origin and the other at the body center. I use genconf to create
a mesh of 4x4x4 unit cells at a distance of 0 0 0.  I thought this is a
better way to simulate a set of crystals.

md.log file:
Max number of graph edges per atom is 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     TRUE
Constants for short-range and fourier stuff:
r1 =      0.000,  rc =      0.500
A  = -8.000e+01,  B  =  1.280e+02,  C  =  3.333e+00, FourPi_V =  8.306e+00
c1 = -1.000e+01,  c2 =  3.000e+01,  c3 = -1.250e+00
c4 = -5.000e+00,  c5 = -3.000e+01,  c6 =  0.000e+00,  N0 =  9.817e-02
Using shifted Lennard-Jones, switch between 0 and 0.5 nm
Cut-off's:   NS: 0.4   Coulomb: 0.5   LJ: 0.5
Generated table with 750 data points for Shift.
Tabscale = 500 points/nm
Generated table with 750 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 750 data points for LJ12Shift.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 128 molecules, 128 charge groups and 128 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 7148.42
There are: 128 Atom
Removing pbc first time
Done rmpbc
Started mdrun on node 0 Fri May 26 10:15:40 2006
Initial temperature: 272.815 K
           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 4 x 4 x 4 cells
calc_bor: cg0=0, cg1=128, ncg=128
CG0[0]=0, CG1[0]=128
CG0[1]=0, CG1[1]=0
calc_bor: cg0=0, cg1=128, ncg=128
CG0[0]=0, CG1[0]=128
CG0[1]=0, CG1[1]=0
There are 128 atoms in your xtc output selection
Large VCM(group rest):      0.00000,     -0.00000,     -0.00000, ekin-cm:
Long Range LJ corr. to Epot:          0, Pres:          0, Vir:          0
   Energies (kJ/mol)
        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)
    3.98375e+07    6.17853e+04    0.00000e+00    0.00000e+00    0.00000e+00
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
    3.98992e+07    3.59069e+04    3.99352e+07    2.26697e+04    1.79321e+09

   Total Virial (kJ/mol)
   -8.16795e+07   -1.31844e+04   -1.31872e+04
   -1.31832e+04   -8.16795e+07   -1.31882e+04
   -1.31904e+04   -1.31864e+04   -8.16795e+07

   Pressure (bar)
    1.79321e+09    5.53395e+05    5.44391e+05
    5.53370e+05    1.79322e+09    5.49020e+05
    5.44463e+05    5.48982e+05    1.79320e+09

   Total Dipole (Debye)
    0.00000e+00    0.00000e+00    0.00000e+00

Large VCM(group rest):      0.00000,     -0.00000,     -0.00000, ekin-cm:
Large VCM(group rest):     -0.00002,      0.00000,      0.00001, ekin-cm:
On 5/25/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> karamyog singh wrote:
> > I am trying to simulate a crystal too. I have a box size of .65 nm and
> > there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm.
> >
> > I get a segmentation fault after mdrun -v. Is an atom with co-ordinates
> > 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system?
> Cubic PBC with side length l means that (x,y,z) is equivalent to
> (x+al,y+bl,z+cl) for any integers a,b and c.
> > What
> > I am trying to ask is, does GROMACS consider these as 2 different atoms
> > placed at the respective positions or do the 2 atoms overlap?
> No. GROMACS takes every atom you give in the .top file and uses it -
> there is no attempt to check for symmetry simplifications such as
> quantum chemistry codes do.
> > What could be the reason for the segmentation fault? Is it because the
> > atoms are too close to each other?
> You're on your own here unless you can provide more information.
> Mark
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