[gmx-users] trjconv -nojump

[mohammad agha]

----- Forwarded Message -----
From: mohammad agha <mra_bu at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, December 27, 2011 8:59 PM
Subject: Re: [gmx-users] trjconv and g_clustsize
 

Thank you very much from your reply.

I found out that my problem is at step "c" (-pbc nojump) because I exercised ngmx after steps "a" and "b" by:
ngmx -f cluster.gro -s cluster.tpr 

and I viewed 2 micelles the same of result of md.trr (or md.xtc).
I studied http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions according to your advice and I think that I should Extract the first frame from the trajectory as reference for removing jumps and then Remove jumps according step "c", but I have a problem about this!
May I ask you to check my steps, please?

1- trjconv -f md.xtc -s md.tpr -o cluster.gro -e 600000 -pbc cluster (and I selected 2 surfactants for clustering group and 0 system for outpup group)

2- grompp -f md.mdp -c cluster.gro -o cluster.tpr -n index.ndx 
Then I did: ngmx -f cluster.gro -s cluster.tpr and I viewed 2 micelles.

3- trjconv -f cluster.gro -s cluster.tpr -dump 0 -o clusterdump.gro (and I selected 0 system for output group)

4- grompp -f md.mdp -c clusterdump.gro -o cluster1.tpr -n index.ndx 

5- trjconv -f cluster.gro -s cluster1.tpr -pbc nojump -o clusternojump.xtc 
Then I did: ngmx -f clusternojump.xtc -s cluster1.tpr  and I had the same previous problem.
May I ask you to help me, please?

Best Regards
Sara




________________________________
 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, December 26, 2011 4:20 PM
Subject: Re: [gmx-users] trjconv and g_clustsize
 

On 12/26/2011 7:53 PM, mohammad agha wrote: 
Dear Prof.
>
>
>I have several questions about trjconv, please help me.
>
>
>In my simulation is created 2 micelles.
>1- When I do 3 steps of micelle clustering as follows:
>
>
>  a- trjconv -f md.xtc -o a_cluster.gro-e 600000 -pbc cluster
> b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr
> c- trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
>
>
>I view 2 micelles according to result of my simulation in VMD but in ngmx isn't view 2 micelles but just is view 1 micelle and reminder of monomers are collected in several groups in different places.
So you don't have a single cluster of atoms... so as trjconv -h
    notes, using -pbc cluster isn't very useful when you don't have a
    cluster of atoms. All my advice of two days ago on this point still
    applies.


Is it right if my criterion be view in VMD and is my micelle clustering correct?
>
It's "correct" if it looks the way you want it to.



>
>2- If I select surfactants for clustering group and system for output group in step (a) and I select system for output group in step (c), command g_clustsize doesn't work correct, consequently, I did under step and made a .xtc file only for surfactants: 
>
>   
>
>    i- trjconv -f md.trr -o md-surfactant.xtc -n index.ndx
>
>    
>
>Then I did steps a, b and c for md-surfactant.xtc and in all of steps I selected surfactants for clustering and output group. Next, I did g_clustsize and it answered me correct.   
>
>May I know that my way is correct, please?
>
>
>
>3- By upper way I have 2 micelles that I got index.ndx file for cluster with maximum size by g_clustsize (maxcluster.ndx).
>May I know how can I use from this for next calculation if I want consider only maximum cluster with all of system (water and ion) in calculations (for example rdf, gyration and etc)?
>
Again I think you are not using the word cluster in the sense the
    GROMACS tools are. Each micelle could be a cluster of atoms, or the
    pair of micelles could be a cluster of micelles. How to use the
    tools will differ according to what you are trying to calculate on
    what kind of cluster. Anyway, the atom numbers do not change with
    the configuration of the atoms, so the same index file group
    identifies the surfactant atoms in each frame. To identify the
    *time* of the configuration with the largest diameter, something
    like g_mindist -max might serve. However you may need to resolve
    your PBC issue first.

Mark

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