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.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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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