[gmx-users] CNT going out of the simulation box after NVT.

[HANNIBAL LECTER]

Use position restraints
<http://www.gromacs.org/Documentation/How-tos/Position_Restraints>, or
freeze the CNT during the NVT dynamics.

On Wed, Mar 4, 2015 at 11:33 PM, soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

>  Dear users,
>                    I am simulating swCNTs in the presence of nucleic acids
> with finite length. I have created the topology of swCNT from the PDB I
> obtained from Tubegen software. I used CHARMM all atomic force field to
> build the topology for both the CNT as well as the DNA. I included the
> CNT.top in the ssDNA.top by modifying atom types. I put the hybrid system
> inside a box of dimension 7.46 x 3.5 x 3.5 nm3 and proceeded fro energy
> minimization after charge neutralization. Energy was minimized within 500
> steps in a steepest descent process. When I took the em.gro file and
> visualized in VMD, portion of the DNA was found outside the box. Hence, I
> did trjconv  with -center to keep the DNA in the center of the box. Then I
> did another energy minimization. The em.gro file this time looked ok in
> VMD. Then, I did the NVT for 1 ns . When I checked the nvt.gro file, now
> the CNT is going outside the box. I cant understand why it is happening.
> The DNA is supposed to wrap around the nanotube. Can anyone help me out
> with this?
>
>
> Thanks and regards,
>
>  Soumadwip Ghosh
>   Research Fellow
>    IITB, Mumbai.
>    India.
> --
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