Re: [gmx-users] Regarding use of harmonic wall model

2020-04-23 Thread Shashank Ranjan Srivastava 
Thank you so much. I will work on it.

Thank you

On Tue, 21 Apr 2020, 18:55 Justin Lemkul,  wrote:

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> On 4/21/20 8:07 AM, Shashank Ranjan Srivastava wrote:
> > Thank you so much Prof. Lemkul for your reply.
> > As I don't know what and how to use this pull code, if you have any idea
> > regarding what you have suggested will be of great help to me.
> > Meanwhile I will read more about it.
>
> General principles here:
> http://www.mdtutorials.com/gmx/umbrella/index.html
>
> Obviously that's a very different approach from what you're trying to do
> but you can learn the basic syntax there.
>
> -Justin
>
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> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
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>
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> http://www.thelemkullab.com
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Re: [gmx-users] Regarding use of harmonic wall model

2020-04-21 Thread Justin Lemkul 




On 4/21/20 8:07 AM, Shashank Ranjan Srivastava wrote:

Thank you so much Prof. Lemkul for your reply.
As I don't know what and how to use this pull code, if you have any idea
regarding what you have suggested will be of great help to me.
Meanwhile I will read more about it.


General principles here: http://www.mdtutorials.com/gmx/umbrella/index.html

Obviously that's a very different approach from what you're trying to do 
but you can learn the basic syntax there.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Regarding use of harmonic wall model

2020-04-21 Thread Shashank Ranjan Srivastava 
Thank you so much Prof. Lemkul for your reply.
As I don't know what and how to use this pull code, if you have any idea
regarding what you have suggested will be of great help to me.
Meanwhile I will read more about it.

Thank You

On Mon, Apr 20, 2020 at 1:14 AM Justin Lemkul  wrote:

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> On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote:
> > Hello everyone,
> > I want to create a gap  between the first and last strand of a beta
> barrel
> > so that I can put a new strand in between.
> > So, I have generated an input file using charmm-gui and using its gromacs
> > production file (production.mdp) to run the simulation. I want to use a
> > harmonic wall model to disrupt the bonding between the first and last
> > strand of the beta barrel but not getting how to do it .
> > I have asked it before as well but I did not get any suggestion.
> > Please kindly help me with this query if anybody has any idea regarding
> > this.
>
> I suggest using the pull code. The implementation of walls in GROMACS
> does not do what you're asking.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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
>
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-- 
Shashank Ranjan Srivastava
Molecular Biophysics Laboratory
Department of Biological Sciences,
IISER-Bhopal,
Madhya Pradesh
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Re: [gmx-users] Regarding use of harmonic wall model

2020-04-19 Thread Justin Lemkul 




On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote:

Hello everyone,
I want to create a gap  between the first and last strand of a beta barrel
so that I can put a new strand in between.
So, I have generated an input file using charmm-gui and using its gromacs
production file (production.mdp) to run the simulation. I want to use a
harmonic wall model to disrupt the bonding between the first and last
strand of the beta barrel but not getting how to do it .
I have asked it before as well but I did not get any suggestion.
Please kindly help me with this query if anybody has any idea regarding
this.


I suggest using the pull code. The implementation of walls in GROMACS 
does not do what you're asking.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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