[gmx-users] trjconv : error

[Nilesh Dhumal]

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
>
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>  Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>