<P>
Sorry for the mistake Tsjerk<BR>
I havent comment on xtc-grps in .mdp file for confirmation pasting .mdp file<BR>
<BR>
title = dpt_prod<BR>
constraints = hbonds<BR>
integrator = md<BR>
dt = 0.002 ; ps !<BR>
nsteps = 3000000 ; total 250 ps.<BR>
nstcomm = 1<BR>
nstxout = 100<BR>
nstlog = 100<BR>
nstenergy = 100<BR>
nstlist = 10<BR>
ns_type = grid<BR>
coulombtype = PME<BR>
rlist = 0.9<BR>
rcoulomb = 0.9<BR>
rvdw = 1.4<BR>
pbc = xyz<BR>
comm_grps = Protein<BR>
; Berendsen temperature coupling is on in two groups<BR>
Tcoupl = Berendsen<BR>
tc-grps = Protein SoL_CL-<BR>
tau_t = 0.1 0.1<BR>
ref_t = 300 300<BR>
; isotropic pressure coupling is off<BR>
Pcoupl = no<BR>
pcoupltype = isotropic<BR>
tau_p = 0.5<BR>
compressibility = 4.5e-5<BR>
ref_p = 1.0<BR>
<BR>
Couls you please tell me how can I select subset of my trajectory file.<BR>
May be this is simple question. <BR>
Thanks in advance. <BR>
<BR>
Hi Minnale,<BR>
<BR>
We do appreciate that english is not your native language (it isn't<BR>
mine either), but please try to write correct, complete sentences.<BR>
That will make it easier to read your posts, understand what you did<BR>
and where you went wrong and how we can, maybe, provide you a<BR>
solution.<BR>
<BR>
Justins reply was right on, and you didn't read his post carefully<BR>
enough. He said to check your xtc-grps, not your tc-grps. xtc-grps, as<BR>
it is unambiguously explained in the manual, determines which sets of<BR>
atoms are saved to the .xtc file. To avoid such confusion, make it a<BR>
habit to paste the .mdp file when you post a problem (after having<BR>
checked the manual, the wiki, and the archives of the list, that is).<BR>
<BR>
Cheers,<BR>
<BR>
Tsjerk<BR>
<BR>
On Sun, Aug 17, 2008 at 7:30 AM, minnale <minnale_gnos at rediffmail.com> wrote:<BR>
><BR>
> Thanks to Justin for his prompt reply<BR>
> in .mdp file mentioned energy groups and tc-grps are protein and sol_cl . I<BR>
> am in doubt that first 250ps of md run it in npt condition later nvt till<BR>
> 7ns finally made into long .xtc file.<BR>
> I tried your suggested way in earlier post but I didnt get it.<BR>
><BR>
> one more doubt I am having is<BR>
> If I load entire .xtc file which contain 7ns trajectory it didnt load<BR>
> Could please tell me why its not loading<BR>
> Thanks in advance.<BR>
><BR>
><BR>
<BR>
On Sat, 16 Aug 2008 Justin A.Lemkul wrote :<BR>
><BR>
><BR>
>minnale wrote:<BR>
>> Hi all,<BR>
>> I intersted in analysing secondary structure of protein by using VMD and performed these steps.<BR>
>>1. First loaded min.gro file and corresponding min.xtc then all equalibration .xtc files till here MD movie has run fine.<BR>
>>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<BR>
>> trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000<BR>
>> selected system, it showed<BR>
>><BR>
>>Fatal error:<BR>
>>Index[2725] 2726 is larger than the number of atoms in the trajectory file (2725)<BR>
><BR>
>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.<BR>
><BR>
>-Justin<BR>
><BR>
>><BR>
>>Could you please give me suggestion if any one have experienced this type of problem<BR>
>>Thanks in advance.<BR>
>><BR>
>><BR>
>><BR>
>>Rediff Shopping <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null><BR>
>><BR>
>><BR>
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><BR>
>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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