[gmx-users] CNT Deformation after Energy Minimization

Dallas Warren dallas.warren at monash.edu
Mon Nov 20 21:36:40 CET 2017

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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