[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ESPResSo-users] Questions regarding FENE/Harmonic potential and Virtual

From: Salvador H-V
Subject: [ESPResSo-users] Questions regarding FENE/Harmonic potential and Virtual Sites
Date: Fri, 11 Jan 2013 14:31:25 -0600

Dear All,

I have a system in 2D composed by a mixture of dumbbells and spheres. The interactions between all particles is the repulsive WCA potential. To set up the system, I just place the particles in random positions and use the l"jforcecap" option to remove overlaps.

Howver, I am facing some troubles during the simulation of this system.  Does anybody could help me with the following situations:

i) When I use rigid bonds to form the dumbbells the simulation runs fine. But If simulate an identical system with the  FENE potential the simulation crash. I have tried different values for the constant K in the bond potential and different parameters during the focecapping cycle but still the same problem. 
The same values for FENE potential work fine in 3D.  Any suggestion?
{0 FENE 100.0 0.2 1.0} {1 SUBT_LJ 100.0 2.0} {0 0 lennard-jones 1.0 1.0 1.122462048309373 0.25 0.0 0.0 0.0}
Haiku2012:06861] *** Process received signal ***
[Haiku2012:06861] Signal: Segmentation fault (11)
[Haiku2012:06861] Signal code: Address not mapped (1)
[Haiku2012:06861] Failing at address: (nil)
[Haiku2012:06861] [ 0] /lib64/ [0x378d00efe0]
[Haiku2012:06861] [ 1] ./Espresso() [0x48a773]
[Haiku2012:06861] [ 2] ./Espresso(calculate_verlet_energies+0x170) [0x487830]
[Haiku2012:06861] [ 3] ./Espresso(energy_calc+0xd2) [0x42bad2]
[Haiku2012:06861] [ 4] ./Espresso(master_energy_calc+0x19) [0x42bea9]
[Haiku2012:06861] [ 5] ./Espresso(tclcommand_analyze_parse_and_print_energy+0xc80) [0x5393d0]
[Haiku2012:06861] [ 6] ./Espresso(tclcommand_analyze+0x15f3) [0x4ea0b3]

ii) Now, I trying to simulate the same system but instead of using rigid/fene bonds, I switch to virtual sites. However, the virtual sites move in 3D. Even if I specify "fix 0 0 1", they still have motion in z coordinate. I add two walls, but I was wondering if it is possible to force the virtual sites to move in "true" 2D.  

iii) Finally, I am interested in the dynamical properties of both type of particles (spheres and dumbbells). I was wondering was is the best option for dynamical properties (Mean square displacement and Mean square rotational displacement ) regarding to thermostating or not the virtual sites.

Thanks a lot in advance!

Kind regards,


reply via email to

[Prev in Thread] Current Thread [Next in Thread]