[gmx-users] Problems with DNA simulation

[Gunnar Widtfeldt Reginsson]

There were no groups specified in the neutralize.mdp file. I specified the
solvent and DNA and it worked.

Thanks.

On Sun, Sep 20, 2009 at 2:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Gunnar Widtfeldt Reginsson wrote:
>
>> Hi. I am new to Gromacs and I am  following the tutorial on
>> http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top<http://wwwuser.gwdg.de/%7Eggroenh/SaoCarlos2008/html/build.html#top>
>>
>> I have managed to get the DNA into a water box. When I run genbox  I use
>> the ffamber_tip4p.gro water model.
>> When I then run:
>> grompp -f neutralize.mdp -c solved.pdb -p topol I get this fatal error:
>> where neutralize.mdp is from the website above.
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.0.5
>> Source code file: readir.c, line: 1463
>>
>> Fatal error:
>> Invalid T coupling input: 0 groups, 2 ref_t values and 2 tau_t values
>> -------------------------------------------------------
>>
>>
>> I have been searching for an explanation to this error but haven't found
>> anything. Can somone please help.
>>
>
> Not without seeing the relevant section of your .mdp file, but it looks
> like you  haven't actually specified any groups to be subject to temperature
> coupling.
>
> -Justin
>
>  Thanks.
>>
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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