[gmx-users] Atom index overflow after adding water

Peggy Yao peggy.yao at gmail.com
Sun Feb 15 01:38:20 CET 2009 

Thank you, Justin!

I found the error message which was embedded in a lot of text. :P

As you said, the atom indexing is not a problem at all. The actual error is:
ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not
implemented

When I changed ns_type to grid, the problem was solved!

Thanks a lot!

Peggy


On Sat, Feb 14, 2009 at 4:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Peggy Yao wrote:
>
>> Unfortunately, no. :( When I tried to add ions to the system using:
>>
>> grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr
>>
>> It return me an error without explanation:
>>
>> processing coordinates...
>> double-checking input for internal consistency...
>>
>> There was 1 note
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.0.2
>> Source code file: grompp.c, line: 864
>>
>> Fatal error:
>> There were 1 error(s) processing your input
>> -------------------------------------------------------
>>
>> Did I make any mistake? I am new to MD simulation and Gromacs. The
>> following are all the steps that I ran until the fatal error:
>>
>>
> Probably.  Search the entire output of grompp for the error message.  I
> don't remember grompp ever reporting a fatal error without printing the
> actual problem somewhere that the user can see.
>
> If you can provide that information, as well as the contents of your .mdp,
> there may be a chance to diagnose what's going on.  As I said before, the
> problem *shouldn't* be the number of atoms in the file.
>
> -Justin
>
>  pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water
>> spce >& pdb2gmx.log
>> # add water
>> editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log
>> genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >&
>> genbox.log
>> # add counter ions
>> grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >&
>> grompp_ion.log
>>
>> Peggy
>>
>> On Sat, Feb 14, 2009 at 3:31 PM, Mark Abraham <mark.abraham at anu.edu.au<mailto:
>> mark.abraham at anu.edu.au>> wrote:
>>
>>
>>
>>    ----- Original Message -----
>>    From: Peggy Yao <peggy.yao at gmail.com <mailto:peggy.yao at gmail.com>>
>>    Date: Sunday, February 15, 2009 10:24 am
>>    Subject: Re: [gmx-users] Atom index overflow after adding water
>>    To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
>>    GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>
>>     > Thank you, Justin!
>>     >
>>     > I changed the output files to .gro.
>>     >
>>     > pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o
>>    1eia.gro -water spce >& pdb2gmx.log
>>     > # add water
>>     > editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log
>>     >
>>    genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >&
>>    genbox.log
>>     >
>>     > However, the overflow error still occurs in the gro file:
>>     >
>>     > 32448SOL    HW299996   9.410   8.282   1.575
>>     > 32449SOL     OW99997   9.923   8.813   0.726
>>     >
>>    32449SOL    HW199998   9.874   8.726   0.735
>>     > 32449SOL    HW299999   9.900   8.856   0.639
>>     > 32450SOL     OW    0   0.018   7.452   0.502
>>     > 32450SOL    HW1    1   0.058   7.543   0.493
>>     > 32450SOL    HW2    2  -0.082   7.460   0.508
>>     >
>>    32451SOL     OW    3   9.507   8.424   1.264
>>     > 32451SOL    HW1    4   9.596   8.379   1.250
>>     >
>>     > What's wrong? Thanks a lot!
>>
>>    Probably nothing. The issue is whether the parsing algorithm in
>>    grompp will handle the situation gracefully. Justin thinks it does.
>>    You should try it and see :-)
>>
>>    Mark
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>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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