In standard force fields for simulations of (bio)molecular systems, the PBC apply only to non-bounded interactions (such as, electrostatic and van der Waals interactions), and not to bonded interactions, such as bond-stretching, angle bending and dihedral energy terms.

PBC apply to everything. If you're dealing with an "infinite" system like a nanotube or some surface, your topology must reflect the fact that bonds are present across periodic boundaries and the software you are using must be able to handle this situation (e.g. GROMACS keyword "periodic_molecules = yes" in the input file). If the VMD plugin isn't smart enough to handle this situation, you'll have to find something more elegant that will generate a proper topology. Because without necessary bonded terms, you'll get spurious nonbonded interactions from atoms that are normally excluded by virtue of being bonded.

Periodic conditions are used to model a system (biomolecules and/or solvent molecules) placed in the unit cell (cubic, rectangle, etc) and considered to have infinitely many images in space. This replication forms an infinite lattice in space (often 3 dimension), enabling simulations to be done using a small number of particles in such way that particles experience forces as if they were in bulk fluid. When dealing with non-bonded interactions, non-bonded cutoffs are used with Minimum Image Convention (MIC), where each atom interacts with at most one image of every other atom in the system, which is repeated infinitely through PBC method. The energy and force is calculated with the closest atom or image. If cutoff is applied the interactions between all pairs of atoms that are further apart than the cutoff value are set to zero, taking into account the closest image. When PBC is used the cutoff should not be so large that a particle sees its own image or the same molecule twice. This has the effect of taking the cutoff value to be not larger than half of simulation box (or shortest side for rectangular shapes) when simulating fluids; when simulating molecules the upper limit on the cutoff may be affected by the molecule size.

On the other hand, when the bonded interaction terms are calculated, the MIC is not used when separation between two bonded atoms is calculated (that's something I wanted to say in my previous answer).

PBC is also employed when saving snapshots for visualization purposes by wrapping atoms (or molecules) if they leave the simulation box.

I just would like to call attention, that provided your Bloch cell is not too large, you might have QM calculations, too. I used e.g. Yamaguchi's MNDO CO - gradient program, though it works in Cartesian coordinates, the force field to be transformed to internal coordinates, via B matrix method (program). It can be resolved, even in case of periodic systems, there are algorithms (formulas) how to perform it.Think it over, would it not be more precise and feasible than MD.

@Justin Lemkuland

Thanks everyone for useful suggestion and specially "Justin Lemkul" for understanding my problem of forcefield assignment.

Dear justin, I was using topotools in order to assign topology  but 1 day, i checked manually by looking into the file that VMD topotools are not considering PBC. and also i saw the post of Axel (developer of topotools ), they discussed the same problem.

So,what software or tool should i use ?? any suggestion ??

What MD engine do you intend to use? I don't know about, and therefore can't vouch for, PSF generators outside CHARMM itself. GROMACS can do this with the x2top program, but it does require careful user input about how bonds are to be defined in the system.

Though I never faced problems like those as we "ab initio" work in internal coordinates, but using standard programs of the B-matrix method you can easily transform Cartesian force fields to internal ones. The only reasonable parametrisation, as everybody knows, can be done in the latters, in case of periodic systems, too, like for example homopolymers with regular structure, if that's the problem you have. Maybe it's not, and you mean something quite different.