[gmx-users] trjconv : error

[gigitang5 at aol.fr]

 Hi Nilesh,
If you need the whole system you maybe don't need to include the -n flag in the tpbconv command it will still create your new tpr file for continuing your work without errors, I had earlier some similar problem. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only..
Gigi

 


 

 

-----E-mail d'origine-----
De : Nilesh Dhumal <ndhumal at andrew.cmu.edu>
A : jalemkul at vt.edu; Discussion list for GROMACS users <gmx-users at gromacs.org>
Envoyé le : Mercredi, 12 Mai 2010 17:47
Sujet : Re: [gmx-users] trjconv : error


Hello Justin,
 As you suggest I used tbpconv

tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr
 and I selected group 0 for system group (In system group all atoms are
present.)

Still I am getting the same error.


I have one more question,
I am working on solvation glucose in ionic liquids. As I told you I want
to show glucose surrounded by cation using iso-surface. After loading
grid.cub file in vmd, all atoms are present. How can I do sothat I can get
only glucose and plot the iso-surface to show cation position.
Can you help me to solve this problem.

Thanks
Nilesh

On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>> I am trying to calculate spatial distribution function (SDF) for my
>> system.
>>
>> 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n
>> test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n
>> test.ndx
>>
>> I am getting the following error for step 2.
>>
>>
>> Fatal error: Index[2385] 2410 is larger than the number of atoms in the
>>  trajectory file (2409).
>>
>> How can I solve this problem?
>> Duirng my simulation I didn't specify xtc_grps  this option in md file.
>>
>>
>
> Then it looks like you must have saved only a subset of your system
> during step 1 or some other post-processing step.  Either save the whole
> system, or use tpbconv to generate a .tpr file that contains only the
> relevant subset of atoms.
>
> -Justin
>
>
>>
>>
>> Thanks
>>
>>
>> Nilesh
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> ========================================
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
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