[gmx-users] CNT Deformation after Energy Minimization

[Aishwarya Smriti]

On individual runs, the protein behaved normally but the CNT deformed there
also. Protein topology was created using OPLS-AA force field of Gromacs
itself and that of CNT was prepared using modified OPLS-AA, taking help
from Andrea Minoia's tutorial.

On Tue, Nov 21, 2017 at 2:05 AM, Dallas Warren <dallas.warren at monash.edu>
wrote:

> Have you ran both systems separately?  Do they behave as they should?
> Where did you get the topologies from?
> 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 20 November 2017 at 22:14, Aishwarya Smriti
> <smritiaishwarya85 at gmail.com> wrote:
> > Hi!
> >
> > I am trying to to do a MD simulation to check interaction of protein with
> > CNT. After combining the two topologies (made individually), I proceeded
> on
> > to Energy Minimization step. The CNT was completely deformed and the
> > protein out of its place after the run. Attached below are the photos for
> > reference. What could be causing this? Please help.
> > Link:
> > https://drive.google.com/drive/folders/1Dy-Y88Dle_
> EZUo00SKkk1etcPOixM9U8?usp=sharing
> > Thanks in advance.
> >
> > Regards,
> > Aishwarya Smriti
> > Senior Undergraduate
> > Department of Chemical Engineering
> > Indian Institute of Technology Delhi
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