[gmx-users] CNT Deformation after Energy Minimization

[Dallas Warren]

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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