Does this give any clue. It shows large PE, KE and temp. Could that be a reason? More information required?<br>
<br>
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.<br>
<br>
md.log file:<br>
----------------------------------------------------------------------------------------------------------------------------------------<br>
Max number of graph edges per atom is 0<br>
Table routines are used for coulomb: TRUE<br>
Table routines are used for vdw: TRUE<br>
Constants for short-range and fourier stuff:<br>
r1 = 0.000, rc = 0.500<br>
A = -8.000e+01, B = 1.280e+02, C = 3.333e+00, FourPi_V = 8.306e+00<br>
c1 = -1.000e+01, c2 = 3.000e+01, c3 = -1.250e+00<br>
c4 = -5.000e+00, c5 = -3.000e+01, c6 = 0.000e+00, N0 = 9.817e-02<br>
Using shifted Lennard-Jones, switch between 0 and 0.5 nm<br>
Cut-off's: NS: 0.4 Coulomb: 0.5 LJ: 0.5<br>
Generated table with 750 data points for Shift.<br>
Tabscale = 500 points/nm<br>
Generated table with 750 data points for LJ6Shift.<br>
Tabscale = 500 points/nm<br>
Generated table with 750 data points for LJ12Shift.<br>
Tabscale = 500 points/nm<br>
Going to determine what solvent types we have.<br>
There are 128 molecules, 128 charge groups and 128 atoms<br>
There are 0 optimized solvent molecules on node 0<br>
There are 0 optimized water molecules on node 0<br>
Center of mass motion removal mode is Linear<br>
We have the following groups for center of mass motion removal:<br>
0: rest, initial mass: 7148.42<br>
There are: 128 Atom<br>
Removing pbc first time<br>
Done rmpbc<br>
Started mdrun on node 0 Fri May 26 10:15:40 2006<br>
Initial temperature: 272.815 K<br>
Step
Time Lambda<br>
0
0.00000 0.00000<br>
<br>
Grid: 4 x 4 x 4 cells<br>
calc_bor: cg0=0, cg1=128, ncg=128<br>
CG0[0]=0, CG1[0]=128<br>
CG0[1]=0, CG1[1]=0<br>
calc_bor: cg0=0, cg1=128, ncg=128<br>
CG0[0]=0, CG1[0]=128<br>
CG0[1]=0, CG1[1]=0<br>
There are 128 atoms in your xtc output selection<br>Large VCM(group
rest): 0.00000,
-0.00000, -0.00000, ekin-cm: 8.92704e-17<br>
Long Range LJ corr. to
Epot: 0,
Pres: 0,
Vir: 0<br>
Energies (kJ/mol)<br>
LJ
(SR) LJ (LR) Disper.
corr. Coulomb (SR) Coulomb (LR)<br>
3.98375e+07
6.17853e+04 0.00000e+00
0.00000e+00 0.00000e+00<br>
Potential Kinetic
En. Total Energy Temperature Pressure
(bar)<br>
3.98992e+07
3.59069e+04 3.99352e+07
2.26697e+04 1.79321e+09<br>
<br>
Total Virial (kJ/mol)<br>
-8.16795e+07 -1.31844e+04 -1.31872e+04<br>
-1.31832e+04 -8.16795e+07 -1.31882e+04<br>
-1.31904e+04 -1.31864e+04 -8.16795e+07<br>
<br>
Pressure (bar)<br>
1.79321e+09 5.53395e+05 5.44391e+05<br>
5.53370e+05 1.79322e+09 5.49020e+05<br>
5.44463e+05 5.48982e+05 1.79320e+09<br>
<br>
Total Dipole (Debye)<br>
0.00000e+00 0.00000e+00 0.00000e+00<br>
<br>
Large VCM(group rest):
0.00000, -0.00000,
-0.00000, ekin-cm: 1.41064e-16<br>
Large VCM(group rest):
-0.00002,
0.00000, 0.00001, ekin-cm:
1.95671e-06<br>
---------------------------------------------------------------------------------------------------------------------------------------------<br><div><span class="gmail_quote">On 5/25/06, <b class="gmail_sendername">Mark Abraham
</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
karamyog singh wrote:<br>> I am trying to simulate a crystal too. I have a box size of .65 nm and<br>> there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm.<br>><br>> I get a segmentation fault after mdrun -v. Is an atom with co-ordinates
<br>> 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system?<br><br>Cubic PBC with side length l means that (x,y,z) is equivalent to<br>(x+al,y+bl,z+cl) for any integers a,b and c.<br><br>> What<br>> I am trying to ask is, does GROMACS consider these as 2 different atoms
<br>> placed at the respective positions or do the 2 atoms overlap?<br><br>No. GROMACS takes every atom you give in the .top file and uses it -<br>there is no attempt to check for symmetry simplifications such as<br>quantum chemistry codes do.
<br><br>> What could be the reason for the segmentation fault? Is it because the<br>> atoms are too close to each other?<br><br>You're on your own here unless you can provide more information.<br><br>Mark<br>_______________________________________________
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