[gmx-users] System Charge in OPLS AA force field.

[Karpurmanjari Kakati]

Hi All,

I am working on a system of polymers having both positive and negative
charge. I am using OPLS AA force field to wokr on it.

While I Vacuum simulated a single chain of the same Charged polymer without
any query.
After being able to do that I proceeded to Vacuum simulation using 5 chains
of the same chain. keeping them at close proximities.

The resultant NVT Run was very unexpected, as I visualised the nvt.gro file
using VMD, the chains were all broken and far part. And was not at all
recognisable. Please help me with this.

This is the NVT.mdp file  used for the purpose:


    ; Run parameters
    integrator = md ; leap-frog integrator
    nsteps = 5000000 ; 2 * 50000 = 100 ps
    dt = 0.001 ; 2 fs
    comm-mode = ANGULAR


    ; Output control
    nstxout = 100 ; save coordinates every 0.2 ps
    nstvout = 100 ; save velocities every 0.2 ps
    nstenergy = 100 ; save energies every 0.2 ps
    nstlog = 100 ; update log file every 0.2 ps


    ; Bond parameters
    continuation = no ; first dynamics run
    constraint_algorithm = lincs ; holonomic constraints
    constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
    lincs_iter = 1 ; accuracy of LINCS
    lincs_order = 4 ; also related to accuracy



    ; Neighborsearching
    ns_type = simple ; search neighboring grid cells
    cutoff-scheme = group
    nstlist = 0 ; 10 fs
    rlist = 0.0 ; short-range neighborlist cutoff (in nm)
    rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm)
    rvdw = 0.0 ; short-range van der Waals cutoff (in nm)


    ; Electrostatics
    coulombtype = Cutoff ; Particle Mesh Ewald for long-range electrostatics
    pme_order = 0 ; cubic interpolation
    fourierspacing = 0.0 ; grid spacing for FFT



    ; Temperature coupling is on
    tcoupl = V-rescale ; modified Berendsen thermostat
    tc-grps = GEL; two coupling groups - more accurate
    tau_t = 0.1 ; time constant, in ps
    ref_t = 310 ; reference temperature, one for each group, in K



    ; Pressure coupling is off
    pcoupl = no ; no pressure coupling in NVT



   ; Periodic boundary conditions
    pbc = no ; 3-D PBC





Also My main motive is to see the behaviour of the polymer in water.

For that I am initially simulating them in vacuum and then plan to solvate
the system with water.. Please let me know if it is the correct way.


Karpurmanjari