[gmx-users] problem with protein secondary structure analysis

Shay Amram shayamra at post.tau.ac.il
Sun Aug 17 11:09:15 CEST 2008

How big is your file? 

Technically you might not be able to load the file if it is larger than you
machine's memory.

One way to deal with this is converting the file (xtc or trr) not to include

If that is indeed the case, I suggest you create a group that contains
everything you have in the simulation except for the solvent and then run:

trjconv -f file.xtc -o file_without_water.xtc -n index.ndx


You will be asked to choose a group - choose the group you created without
the water.

Now do the same to your .gro file (so there would be the same number of
atoms in gro and in the xtc), and you should be able to load the entire
"no-water" xtc without problems.





From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of minnale 
Sent: Sunday, August 17, 2008 08:30 AM
To: gmx-users1
Subject: Re: Re: [gmx-users] problem with protein secondary structure


Thanks to Justin for his prompt reply
in .mdp file mentioned energy groups and tc-grps are protein and sol_cl . I
am in doubt that first 250ps of md run it in npt condition later nvt till
7ns finally made into long .xtc file.
I tried your suggested way in earlier post but I didnt get it. 

one more doubt I am having is
If I load entire .xtc file which contain 7ns trajectory it didnt load  
Could please tell me why its not loading 
Thanks in advance.

On Sat, 16 Aug 2008 Justin A.Lemkul wrote :
>minnale wrote:
>>  Hi all,
>>    I intersted in analysing secondary structure of protein by using VMD
and performed these steps.
>>1. First loaded min.gro file and corresponding min.xtc then all
equalibration .xtc files till here MD movie has run fine.
>>2. I had long trajectory in a single file, so cut it down into
subtrajectories with 1ns interval by using *trjconv command and issued like
>>  trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000
>>  selected system, it showed
>>Fatal error:
>>Index[2725] 2726 is larger than the number of atoms in the trajectory file
>You've only saved a subset of your trajectory.  Check the xtc-grps in your
.mdp file.  You can use trjconv if you have a reference structure that
matches the contents of your trajectory.
>>Could you please give me suggestion if any one have experienced this type
of problem
>>Thanks in advance.
>>Rediff Shopping
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>-- ========================================
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080


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