Re: [gmx-users] Regarding trjconv

[Ali Khodayari]

Thank you Justin.
I tried to define a reference group having the desired orientation and use
-fit. But the box rotates as well. I need to keep the box as it is and just
rotate the solute. Using -fit prompts me to choose the group for least
squares fit and the output, only. When I use -princ in editconf, it orients
the crystal in z direction perfectly. The only problem is that the box
rotates as well, and is not well aligned along the same direction. Any
suggestions?
Best,
Ali


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Justin
Lemkul
Sent: zondag 2 december 2018 17:38
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Regarding trjconv



On 12/2/18 11:22 AM, Ali Khodayari wrote:
> Dear all,
>
>   
>
> I am trying to re-center and re-orient an md resulted solute in a box. 
> Yet, I need the box to hold its position and I only need a group of 
> atoms to align along z-direction. Trjconv centers the group in the box 
> but the desired sub-group has a slight inclination which is needed to 
> be oriented along z axis. Is there any particular trick to do this? 
> Maybe in combination with editconf?
>
>   

trjconv -fit with a suitable index group that defines the orientation you
want.

-Justin

--
==

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

Virginia Tech Department of Biochemistry
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Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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==

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Re: [gmx-users] Regarding trjconv

[Justin Lemkul]

On 12/2/18 11:22 AM, Ali Khodayari wrote:

Dear all,

  


I am trying to re-center and re-orient an md resulted solute in a box. Yet,
I need the box to hold its position and I only need a group of atoms to
align along z-direction. Trjconv centers the group in the box but the
desired sub-group has a slight inclination which is needed to be oriented
along z axis. Is there any particular trick to do this? Maybe in combination
with editconf?

  


trjconv -fit with a suitable index group that defines the orientation 
you want.


-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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[gmx-users] Regarding trjconv

[Ali Khodayari]

Dear all,

 

I am trying to re-center and re-orient an md resulted solute in a box. Yet,
I need the box to hold its position and I only need a group of atoms to
align along z-direction. Trjconv centers the group in the box but the
desired sub-group has a slight inclination which is needed to be oriented
along z axis. Is there any particular trick to do this? Maybe in combination
with editconf?

 

Best,

Ali

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Re: [gmx-users] Regarding trjconv

[Gregory Poon]

On 11/17/2016 10:19 AM, Justin Lemkul wrote:



On 11/17/16 10:13 AM, Apramita Chand wrote:

Dear All,
Thanks for your explanation, Erik. I just want to know whether applying
trjconv will affect my calculations of other values like radial
distribution functions ,hydrogen bond properties.
Before applying trjconv,my protein molecule appears to be shifted partly
out of the box . Should I be applying trjconv in this situation before
calculation of properties? Is it necessary at all?



Nearly all GROMACS tools handle PBC automatically.  Only 
position-dependent properties like RMSD, RMSF, covariance, etc. are 
impacted by not accounting for PBC.  Anything related to distances 
like RDF, H-bonds, etc. requires no correction, but even if you do use 
trjconv, the results should come out the same.


-Justin



I have also noticed that if use a PBC-corrected .xtc file for hbond 
against solvent molecules, it will often generate an error or crash the 
tool, which does not occur without trjconv.


Gregory
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Re: [gmx-users] Regarding trjconv

[Justin Lemkul]

On 11/17/16 10:13 AM, Apramita Chand wrote:

Dear All,
Thanks for your explanation, Erik. I just want to know whether applying
trjconv will affect my calculations of other values like radial
distribution functions ,hydrogen bond properties.
Before applying trjconv,my protein molecule appears to be shifted partly
out of the box . Should I be applying trjconv in this situation before
calculation of properties? Is it necessary at all?



Nearly all GROMACS tools handle PBC automatically.  Only position-dependent 
properties like RMSD, RMSF, covariance, etc. are impacted by not accounting for 
PBC.  Anything related to distances like RDF, H-bonds, etc. requires no 
correction, but even if you do use trjconv, the results should come out the same.


-Justin

--
==

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] Regarding trjconv

[Apramita Chand]

Dear All,
Thanks for your explanation, Erik. I just want to know whether applying
trjconv will affect my calculations of other values like radial
distribution functions ,hydrogen bond properties.
Before applying trjconv,my protein molecule appears to be shifted partly
out of the box . Should I be applying trjconv in this situation before
calculation of properties? Is it necessary at all?


Regards
Apramita
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Re: [gmx-users] Regarding trjconv

[Erik Marklund]

Dear Aparamita,

trjconv can enable or preclude subsequent analysis of trajectories, depending 
on what you want to do. For example, by fitting chosen groups to a reference 
structure. By centering your protein, you effectively remove all lateral 
diffusion, so it’s not surprising that a very low diffusion coefficient is 
reported for the processed trajectory.

Kind regards,
Erik

> On 17 Nov 2016, at 08:53, Apramita Chand  wrote:
> 
> Dear All,
> I had one doubt regarding g_trjconv which I used to center my protein after
> simulation. I got different diffusion values when I used the .xtc file
> before and after applying trjconv. Which one should be used?  Is trjconv
> just for visualisation or is necessary for analysis too? Does it change the
> values or interactions in any way?
> For example, the diffusion values that I got were
>  Before trjconv   After Trjconv
> Urea -  1.6628  2.089
> Protein  -0.09270.000108
> Water   2.513  2.59
> 
> Please advise. Which values should be taken?
> 
> Regards
> Apramita
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[gmx-users] Regarding trjconv

[Apramita Chand]

Dear All,
I had one doubt regarding g_trjconv which I used to center my protein after
simulation. I got different diffusion values when I used the .xtc file
before and after applying trjconv. Which one should be used?  Is trjconv
just for visualisation or is necessary for analysis too? Does it change the
values or interactions in any way?
For example, the diffusion values that I got were
  Before trjconv   After Trjconv
Urea -  1.6628  2.089
Protein  -0.09270.000108
Water   2.513  2.59

Please advise. Which values should be taken?

Regards
Apramita
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