[gmx-users] trjconv : error

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> 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.
> 

By selecting "System," you are essentially generating the same .tpr file.  Using 
tpbconv to get around this problem is potentially dangerous, since I don't know 
what groups you're trying to analyze, what's in your trajectory, etc.  The 
better option is to tell us what you've been doing all along, with details of 
groups selected, etc.  The bottom line is you are trying to analyze a trajectory 
that (somehow) doesn't have all the atoms the .tpr file does, and when you're 
trying to run analysis on whatever groups you have, the index values are 
inconsistent.

> 
> 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.
> 

No clue.  What are the prompts from g_spatial?  What are the groups you are 
telling it to analyze and/or output?

-Justin

> 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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> 
> 
> 

-- 
========================================

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

========================================