[gmx-users] problem with protein secondary structure analysis

minnale minnale_gnos at rediffmail.com
Sun Aug 17 09:14:13 CEST 2008

Sorry for the mistake Tsjerk
I havent comment on xtc-grps in .mdp file for confirmation pasting .mdp file

title               =  dpt_prod
constraints         =  hbonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  3000000  ; total 250 ps.
nstcomm             =  1
nstxout             =  100
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  1.4
pbc                 =  xyz
comm_grps           =  Protein
; Berendsen temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps             =  Protein   SoL_CL-
tau_t               =  0.1       0.1
ref_t               =  300       300
; isotropic pressure coupling is off
Pcoupl              =  no
pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
Couls you please tell me how can I select subset of my trajectory file.
May be this is simple question. 
Thanks in advance.  

Hi Minnale,

We do appreciate that english is not your native language (it isn't
mine either), but please try to write correct, complete sentences.
That will make it easier to read your posts, understand what you did
and where you went wrong and how we can, maybe, provide you a

Justins reply was right on, and you didn't read his post carefully
enough. He said to check your xtc-grps, not your tc-grps. xtc-grps, as
it is unambiguously explained in the manual, determines which sets of
atoms are saved to the .xtc file. To avoid such confusion, make it a
habit to paste the .mdp file when you post a problem (after having
checked the manual, the wiki, and the archives of the list, that is).



On Sun, Aug 17, 2008 at 7:30 AM, minnale <minnale_gnos at rediffmail.com> wrote:
> 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 this
>>   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 (2725)
>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.
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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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