[gmx-users] CNT Deformation after Energy Minimization

[Dallas Warren]

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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.