[gmx-users] Time step problem on coarse-grained LJ chain

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 24 23:05:20 CET 2011

Hi Chrysostomos,

To understand this, you have to understand how jumps are removed. I
explained that before, and it's in the archive somewhere. The bottom
line is that jumps can't be removed properly when intervals between
frames are too large, or the changes in position are too large
relative to the size of the box.



2011/11/24 Tomy van Batis <tomyvanbatis at gmail.com>:
> Dear all
> I am trying to simulate a Lennard-Jones coarse-grained polymer melt. Until
> know I simulated only one chain, in order to check if the parameters I used
> are OK.
> I simulated one chain of 50 LJ particles with ε=1KJ/mol, m=1gr/mol, σ=1nm.
> This means that my characteristic time of the system τ=σ(m/ε)1/2 is τ=1ps.
> I am using RIGID bonds between the particles also with length σ=1nm.
> I have seen in many papers which are using similar systems that the time
> step they use is Dt=0.01τ.
> When I use Dt=0.01τ I don't get any error messages in my .log file or in the
> resulting .gro file.
> The problem that I have is when I am trying to convert my .xtc file to .pdb
> in order to visualize it in VMD.
> When I use:
> trjconv -f  ***.xtc   -s  ***.tpr      -o  ***.pdb     -pbc whole
> the trajectory looks fine.
> BUT, when I use
> trjconv    -f  ***.xtc    -s ***.tpr   -o ***.pdb     -pbc nojump
> , it seems the chain is blowing after few steps (the bonds break and the
> particles spread in every direction).
> I would think that for a single chain, these two options of trjconv should
> not make such a difference.
> I used a relatively big box for the simulation (10 X 10 X 60). The strange
> think is that I don't have this problem when I increase the box size (to
> 50X50X60) , or of course when I decrease the time step.
> Is it possible that I am not able to use such a large time-step in GROMACS,
> or is it something with the trjconv that I don't understand ?
> Thanks in advance
> Best Regards, Chrysostomos
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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