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

[Dallas Warren]

This is an PBC artefact, and the molecules are not actually broken.
Use "gmx trjconv -pbc whole" to make molecules broken across the PBC
like this whole again.

An illustration of this you can find at
https://twitter.com/dr_dbw/status/1066843191159050240

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Thu, 22 Nov 2018 at 22:52, 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.