[gmx-users] Problem - How to center a protein in a CG simulation

Carlos Navarro Retamal cnavarro at utalca.cl
Tue Nov 11 02:52:39 CET 2014

Dear Justin,
It worked! :D
Thanks a lot.
I first preprocess  the whole trajectory,  
> trjconv -f dynamic-NO-Elastic.xtc -s equilibration.tpr -pbc mol  

And after that i center the protein  

> trjconv -f trajout.xtc -s equilibration.tpr -pbc mol -center -skip 50 -o test.xtc
In order to extract the last frame i used the following command:

> trjconv -f test.xtc -sep -o LastFrame.gro

The only ‘issue’ was that the frames i saved with -sep content the description of each atom as follows:

>     1LYS     BB    1   5.4   6.9   8.4
>     1LYS    SC1    2   5.3   7.2   8.5
>     1LYS    SC2    3   5.0   7.3   8.6
>     2ARG     BB    4   5.1   6.8   8.5
>     2ARG    SC1    5   5.1   6.6   8.7
>     2ARG    SC2    6   5.0   6.5   9.0

so i got an error with initram. To avoid this i performed a minimisation of this lastFrame.gro file in order to obtain the correct description of each atom. After that, FINALLY, the backward process worked :D

Thanks to all of you :D

ps- During the CG simulation using Elastic-Network i saw big movements of the K2P protein, and when i compared it with respect to the inicial AA model i saw how a part of the CAP of the K2P channel is completely rotate to another side of the protein.
 I used 500 kj/mol^-1/nm^-2 as the tutorial suggest.  
Should i increase the elastic force constant to 1000 (or even more), or instead try ElNeDyn?  
I didn’t want to use this approximation, since the tutorial emphasise that using it will be huge change on the martini ff.
Best regards to all of you,
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

On Monday, November 10, 2014 at 8:45 PM, Justin Lemkul wrote:

> On 11/10/14 10:01 AM, Carlos Navarro Retamal wrote:
> > nobody?
> > if there is not a way to do this at this moment (after the simulation) is there a way to apply a restraint to maintain fix the protein in the middle of the POPC bilayer (other than elastic network) during the MD simulation in order to avoid this problem?
> >  
> I don't know why the -center option isn't working. That's precisely what it  
> does. Other things to try:
> 1. Often I find that PBC routines do not work well when dealing with a single  
> coordinate file. Processing the trajectory, then extracting the frame(s) of  
> interest works all the time.
> 2. Try the -fit transxy option of trjconv. It's designed for interfacial and  
> membrane systems.
> -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
> jalemkul at outerbanks.umaryland.edu (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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