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

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

[gmx-users] Problem with pdb2gmx in gromacs 4.5.3

Dear Gromacs users I have a very strange problem when using pdb2gmx in the gromacs 4.5.3. I looked up the mailing list but I can't find something similar. I have in a .pdb file a crystalline substrate consisting of Si particles. By running in previous gromacs version (i.e. gromacs 3.3) : *pdb2g

[gmx-users] Problem when running in many nodes

Dear all The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I experience some difficulties when running in parallel. Initially, my simulation box has dimensions : * 3.30507 2.67145 41.15800* and it consists of 25 polymers chains with 50 beads/chain When I run NVT using 8 or 1

[gmx-users] Reduced Units

Dear all I would like to do coarse-grained simulations using reduced LJ units. As I can see in the manual, this is possible, but I don't understand how... I use the Gromos96 53a6 force field. In the *ffG53a6nb.itp *the* σ* and *ε* are in *(nm*) and *(KJ/mol*) Also in the *ffG53a6.atp* the *mas*s

[gmx-users] Problem with COM movement

Dear all I have the following system: Two substrates (which are FCC lattices consisting of LJ particles) in a distance of 50nm and between these substrates I put completely stretched polymer chains. The substrates are parallel to xy plane and the chains are vertical. The length of the stretched c

Re: [gmx-users] How to define Center of Mass velocity of a specific group

On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul wrote: > > > Tomy van Batis wrote: > >> Dear all >> >> I have a system consisting of 2 substrates (20 nm distance between them) >> and inside them there are polymer chains. I would like during my NVT >>

[gmx-users] How to define Center of Mass velocity of a specific group

Dear all I have a system consisting of 2 substrates (20 nm distance between them) and inside them there are polymer chains. I would like during my NVT simulations the substrates NOT to move (I suppose I have to put the velocity of the COM of it's substrate to be zero). Does anyone know how to do