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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