Fw: [gmx-users] trjconv in martini

[mohammad agha]

----- Forwarded Message -----
From: mohammad agha <mra_bu at yahoo.com>
To: Tsjerk Wassenaar <tsjerkw at gmail.com> 
Sent: Friday, December 30, 2011 3:16 PM
Subject: Re: [gmx-users] trjconv in martini
 

Hi Tsjerk,

Thank you very much from your reply, I have a problem about ./xtcrev.py 1a.xtc > 1a-rev.xtcI did ./xtcrev.py 1a.xtc > 1a-rev.xtc but it answered me:
from: can't read /var/mail/struct
./xtcrev.py: line 21: import: command not found
./xtcrev.py: line 22: import: command not found
./xtcrev.py: line 24: syntax error near unexpected token `('
./xtcrev.py: line 24: `def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])'

May I ask you to help me?

Best Regards 

Sara


________________________________
 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, December 30, 2011 3:01 PM
Subject: Re: [gmx-users] trjconv in martini
 
Hi Sara,

Assuming you have saved the script xtcrev.py:

# Get a clustered reference frame
trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 200000

# Extract the first part of the trajectory
trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999

# Reverse it
./xtcrev.py 1a.xtc > 1a-rev.xtc

# Remove jumps
trjconv -s cluster.gro -f 1a-rev.xtc -o 1a-rev-clus.xtc -pbc nojump

# Reverse it again
./xtcrev.py 1a-rev-clus.xtc > 1a-clus.xtc

# Extract the second part of the trajectory
trjconv -s md.tpr -f md.trr -o 1b.xtc -b 200000

# Remove jumps
trjconv -s cluster.gro -f md.trr -pbc nojump -o 1b-clus.xtc

# Put the two together
trjcat -f 1a-clus.xtc 1b-clus.xtc -o clustered.xtc

# Hope it helps

# Tsjerk



On Fri, Dec 30, 2011 at 12:01 PM, mohammad agha <mra_bu at yahoo.com> wrote:
> Dear gromacs users,
>
> At the first I thank from Tsjerk and Mark because of their answers to me but
> unfortunately I don't understand that where is my mistake, still?
> I work with MARTINI coarse-grained and I have a problem after -pbc nojump!
> My simulation lasts 600 ns and 2 micelles are created from 200 ns and remain
> during 400 ns, then my micelles isn't formed at the end of the trajectory.
> My commands are:
> 1- trjconv -f md.trr -s md.tpr -n index.ndx -e 600000 -pbc cluster -o 1.gro
>  In this step I viewed 2 micelles from 200 ns to 600 ns by ngmx -f 1.gro -s
> md.tpr, so I have 2 micelles and -pbc cluster works me well and has been
> removed box boundaries from my system but I saw very jumps in my system.
> Okay?
> 2- grompp -f md.mdp -c 1.gro -o 1.tpr -n
 index.ndx
> 3- trjconv -f 1.gro -s 1.tpr -o 2.xtc -pbc nojump
> After this step, had been removed jumps but I didn't see 2 micelles in 200
> ns, I saw that my monomers were collected as groups in the different places.
> (This is bad and I don't know where is my mistake and what should I do to
> solve my problem!)
> After this, to solve my problem, I did:
> 4- trjconv -f 2.xtc -s 1.tpr -o 3.xtc -pbc mol
> In this step, I viewed 2 micelles from 200 ns to 600 ns and had been removed
> jumps but existed boundaries of box, means my micelles that leaves a
> simulation box by, say, the right-hand face, then enters the simulation box
> by the left-hand face.
> May I know can I start analysis of my system with 3.xtc? Is it good? If it
> isn't good, Please help me for this problem with nojump.
>
> Thank you very much in advance
> Best Regards
>
 Sara
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced
 Materials
University of Groningen
The Netherlands
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