Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

[Vytautas Rakeviius]

I altered distance restraints according to your comment into:
[ distance_restraints ]
 195 281 1 1 1 0.4 0.44 0.48 1000Still get same issue that 195 and 281 even 
move away from each other.
Here link to all files again, hopefully it will not be distorted.
http://www.mediafire.com/file/ruaxx6nbj2qpvm6/MD_4AK0_test_pub.tar.bz2
How can I drag 195 and 281closer with distance restraints? (not necessary as 
close as 0.2 nm)

 

On Wednesday, March 15, 2017 2:54 PM, Justin Lemkul  wrote:
 

 

On 3/15/17 6:28 AM, Vytautas Rakeviius wrote:
> Hello, I try to add distance restraints on two TYR OH groups so that they are 
> together in the end like this:
>
> [ distance_restraints ]
>  195 281 1 1 1 0.2 0.22 0.24 1000
> But it does not work at least over time frame I tested, they even go further 
> away from each other.
>
> Here I share my all files:MD_4AK0_test_pub.tar.bz2

That's not a valid link.

If you're trying to keep 2 oxygen atoms at a distance of 0.2 nm, that's well 
within the (likely) repulsive wall of the LJ potential, as well as being 
repulsive from the perspective of the electrostatics.  You'll either need a 
massive biasing force to keep them close, or develop a different way to keep 
them at such a distance.  Why are you imposing this bias, and at such a short 
distance?

-Justin

> System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt 
> -p topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in 
> wrong way?
>
> |
> |
> |
> |  |    |
>
>    |
>
>  |
> |
> |  |
> MD_4AK0_test_pub.tar.bz2
>  MediaFire is a simple to use free service that lets you put all your photos, 
>documents, music, and video in a si...  |  |
>
>  |
>
>  |
>
>
>

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


   
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Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

[Justin Lemkul]

On 3/15/17 6:28 AM, Vytautas Rakeviius wrote:

Hello, I try to add distance restraints on two TYR OH groups so that they are 
together in the end like this:

[ distance_restraints ]
 195 281 1 1 1 0.2 0.22 0.24 1000
But it does not work at least over time frame I tested, they even go further 
away from each other.

Here I share my all files:MD_4AK0_test_pub.tar.bz2


That's not a valid link.

If you're trying to keep 2 oxygen atoms at a distance of 0.2 nm, that's well 
within the (likely) repulsive wall of the LJ potential, as well as being 
repulsive from the perspective of the electrostatics.  You'll either need a 
massive biasing force to keep them close, or develop a different way to keep 
them at such a distance.  Why are you imposing this bias, and at such a short 
distance?


-Justin


System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p 
topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in wrong 
way?

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MD_4AK0_test_pub.tar.bz2
 MediaFire is a simple to use free service that lets you put all your photos, 
documents, music, and video in a si...  |   |

  |

  |





--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

[gmx-users] Distance restraints on two TYR OH groups so that they are together

[Vytautas Rakeviius]

Hello, I try to add distance restraints on two TYR OH groups so that they are 
together in the end like this:

[ distance_restraints ]
 195 281 1 1 1 0.2 0.22 0.24 1000
But it does not work at least over time frame I tested, they even go further 
away from each other.

Here I share my all files:MD_4AK0_test_pub.tar.bz2
System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p 
topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in wrong 
way?
  
|  
|   
|   
|   ||

   |

  |
|  
|   |  
MD_4AK0_test_pub.tar.bz2
 MediaFire is a simple to use free service that lets you put all your photos, 
documents, music, and video in a si...  |   |

  |

  |

 
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