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

[Justin Lemkul]

On 3/4/15 11:33 PM, soumadwip ghosh 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?
>

There is no such thing as "outside" a periodic system.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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