[gmx-users] CNT Deformation after Energy Minimization

[Aishwarya Smriti]

Will try it. Thanks for help!

On Tue, Nov 21, 2017 at 3:02 AM, Dallas Warren <dallas.warren at monash.edu>
wrote:

> No idea, never used it.
>
> EM will not move an entire molecule in the manner in which those two
> images you shared imply.
>
> Check the coordinate files closely, plus whether it is a PBC artefact,
> and double check that you fed the correct coordinate file to grompp.
>
> 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 21 November 2017 at 08:13, Aishwarya Smriti
> <smritiaishwarya85 at gmail.com> wrote:
> > The protein and CNT were placed together using PACKMOL. Could that
> create a
> > difference?
> >
> > On Tue, Nov 21, 2017 at 2:27 AM, Dallas Warren <dallas.warren at monash.edu
> >
> > wrote:
> >
> >> Fact that CNT deforms by itself says you need to fix that topology
> >> before going any further.
> >>
> >> As for the displacement of the protein you saw when running the EM,
> >> it's either a PBC artefact or the protein was not placed where you
> >> thought it was placed.
> >> 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 21 November 2017 at 07:54, Aishwarya Smriti
> >> <smritiaishwarya85 at gmail.com> wrote:
> >> > 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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