Re: [gmx-users] Multiple runs for same system

[Justin Lemkul]

On 2/25/18 6:07 PM, Dr. Seema Mishra wrote:

Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. 
Right?


However you want to do it, either by specifying a seed or letting grompp 
generate one. Some prefer the former for reproducibility, but given all 
the things that can affect binary reproducibility, I don't think it's a 
big concern.



After this, how many runs will be performed? One? Then after the production run 
is finished, start it again with gen_seed=-1 for the second run?


Each .tpr specifies one initial set of conditions for a simulation. If 
you want another simulation, generate another .tpr that specifies a 
different set of conditions.


-Justin


This is to be done for 3 independent runs for same protein-ligand system.

Seema
  


 On Monday, 26 February 2018 4:16 AM, Justin Lemkul  wrote:
  

  
Multiple runs are typically initiated simply by changing gen_seed when

generating velocities at the outset of equilibration.

As for clustering, you'll have to explain what you mean. Clustering
ligand poses? Protein? What? Does a Google search for "GROMACS
clustering" or the help information for gmx cluster point you to
anything useful

-Justin

On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:

Or just direct me to the steps written anywhere

       On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
 wrote:
   


   Hi, Can anyone tell me the steps and commands for performing multiple runs 
of 50 ns for same protein-ligand system? Also the clustering for further 
analyses. Thanks.


 


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Multiple runs for same system

[Dr. Seema Mishra]

Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. 
Right?
After this, how many runs will be performed? One? Then after the production run 
is finished, start it again with gen_seed=-1 for the second run?

This is to be done for 3 independent runs for same protein-ligand system.

Seema
 

On Monday, 26 February 2018 4:16 AM, Justin Lemkul  wrote:
 

 
Multiple runs are typically initiated simply by changing gen_seed when 
generating velocities at the outset of equilibration.

As for clustering, you'll have to explain what you mean. Clustering 
ligand poses? Protein? What? Does a Google search for "GROMACS 
clustering" or the help information for gmx cluster point you to 
anything useful

-Justin

On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:
> Or just direct me to the steps written anywhere
>
>      On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
> wrote:
>  
>
>  Hi, Can anyone tell me the steps and commands for performing multiple runs 
>of 50 ns for same protein-ligand system? Also the clustering for further 
>analyses. Thanks.
>
>
>    

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Multiple runs for same system

[Justin Lemkul]

Multiple runs are typically initiated simply by changing gen_seed when 
generating velocities at the outset of equilibration.


As for clustering, you'll have to explain what you mean. Clustering 
ligand poses? Protein? What? Does a Google search for "GROMACS 
clustering" or the help information for gmx cluster point you to 
anything useful


-Justin

On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:

Or just direct me to the steps written anywhere

 On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
 wrote:
  


  Hi, Can anyone tell me the steps and commands for performing multiple runs of 
50 ns for same protein-ligand system? Also the clustering for further analyses. 
Thanks.





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Multiple runs for same system

[Dr. Seema Mishra]

Or just direct me to the steps written anywhere 

On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
 wrote:
 

 Hi, Can anyone tell me the steps and commands for performing multiple runs of 
50 ns for same protein-ligand system? Also the clustering for further analyses. 
Thanks. 


   
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