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<div> <font size="2"><font face="Arial, Helvetica, sans-serif">Hi Nilesh,<br>
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..<br>
Gigi<br>
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<div style="font-family: arial,helvetica; font-size: 10pt; color: black;">-----E-mail d'origine-----<br>
De : Nilesh Dhumal <ndhumal@andrew.cmu.edu><br>
A : jalemkul@vt.edu; Discussion list for GROMACS users <gmx-users@gromacs.org><br>
Envoyé le : Mercredi, 12 Mai 2010 17:47<br>
Sujet : Re: [gmx-users] trjconv : error<br>
<br>
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<pre style="font-size: 9pt;"><tt>Hello Justin,<br>
As you suggest I used tbpconv<br>
<br>
tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr<br>
and I selected group 0 for system group (In system group all atoms are<br>
present.)<br>
<br>
Still I am getting the same error.<br>
<br>
<br>
I have one more question,<br>
I am working on solvation glucose in ionic liquids. As I told you I want<br>
to show glucose surrounded by cation using iso-surface. After loading<br>
grid.cub file in vmd, all atoms are present. How can I do sothat I can get<br>
only glucose and plot the iso-surface to show cation position.<br>
Can you help me to solve this problem.<br>
<br>
Thanks<br>
Nilesh<br>
<br>
On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote:<br>
><br>
<br>
><br>
> Nilesh Dhumal wrote:<br>
><br>
>> Hello,<br>
>> I am trying to calculate spatial distribution function (SDF) for my<br>
>> system.<br>
>><br>
>> 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n<br>
>> test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n<br>
>> test.ndx<br>
>><br>
>> I am getting the following error for step 2.<br>
>><br>
>><br>
>> Fatal error: Index[2385] 2410 is larger than the number of atoms in the<br>
>> trajectory file (2409).<br>
>><br>
>> How can I solve this problem?<br>
>> Duirng my simulation I didn't specify xtc_grps this option in md file.<br>
>><br>
>><br>
><br>
> Then it looks like you must have saved only a subset of your system<br>
> during step 1 or some other post-processing step. Either save the whole<br>
> system, or use tpbconv to generate a .tpr file that contains only the<br>
> relevant subset of atoms.<br>
><br>
> -Justin<br>
><br>
><br>
>><br>
>><br>
>> Thanks<br>
>><br>
>><br>
>> Nilesh<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
><br>
> --<br>
> ========================================<br>
><br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]vt.edu | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
><br>
> ========================================<br>
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</tt></pre>
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