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.war...@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 <ch18resch01...@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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
