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

[Karpurmanjari Kakati]

Hi,
Does that mean that I will not be able to visualize the system upon end of
NVT step?
Because "gmx trjconv -pbc whole " can be used one MD run is completed? or
can it be performed before it is done?

Please let me know.
Also is this the wholesome Command?

On Thu, Nov 22, 2018 at 5:21 PM Karpurmanjari Kakati <
ch18resch01002 at iith.ac.in> wrote:

> 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
>
>
>