[gmx-users] Crashes during protein-ligand simulation

[Justin A. Lemkul]

On 7/8/12 6:57 AM, James Starlight wrote:
> Justin,
>
> unfortunately my last system have also been crashed after 35ns of
> simulation with the links warnings accompanied by the error
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> This time I've devided all functional groups of my ADENOSINE ligand
> into separate charge groups in topol.itp.
>

Note that these charges are not the same as the adenosine moiety of ATP, which 
is standard in the Gromos96 force fields.  Perhaps you should re-evaluate some 
charges (see aminoacids.rtp for the existing ATP implementation).

> ;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
>      1    NT    1    ADN     N6    1   -0.844  14.0067
>      2     H    1    ADN    H11    1    0.422   1.0080
>      3     H    1    ADN    H12    1    0.422   1.0080      ;  0.000
>      4     C    1    ADN     C8    2    0.097  12.0110
>      5    HC    1    ADN    H01    2    0.177   1.0080
>      6    NR    1    ADN     N3    2   -0.642  14.0067
>      7     C    1    ADN     C4    2    0.175  12.0110
>      8     C    1    ADN     C5    2    0.092  12.0110
>      9    NR    1    ADN     N7    2   -0.556  14.0067
>     10     C    1    ADN     C6    2    0.657  12.0110      ;  0.000
>     11     C    1    ADN    C5'    3   -0.677  12.0110
>     12     C    1    ADN    C4'    3    0.834  12.0110
>     13    OE    1    ADN    O4'    3   -0.248  15.9994
>     14     C    1    ADN    C1'    3   -0.558  12.0110
>     15     C    1    ADN    C2'    4    0.603  12.0110
>     16     C    1    ADN    C3'    5   -0.212  12.0110
>     17    NR    1    ADN     N9    3    0.415  14.0067
>     18    OA    1    ADN    O2'    4   -0.606  15.9994
>     19     H    1    ADN    H08    4    0.482   1.0080
>     20    OA    1    ADN    O3'    5   -0.606  15.9994
>     21     H    1    ADN    H06    5    0.482   1.0080
>     22    OA    1    ADN    O5'    3   -0.246  15.9994
>     23     H    1    ADN    H03    3    0.337   1.0080      ; -0.000
>     24     C    1    ADN     C2    6    0.502  12.0110
>     25    HC    1    ADN    H10    6    0.106   1.0080
>     26    NR    1    ADN     N1    6   -0.608  14.0067      ;  0.000
>
>
> Also I've done proper equilibration in tho steps (I've used 1fs
> integrator steps on both stages of equilibration)
> 1- I've made equilibration with posres ( 500ps) on protein backbone
> atoms as well as ligand with x-ray water
>
> 2- The next step (5ns) was done without posres only with smaller
> integrator steps.
>
> What another possible sollutions could be ?
>

Try some diagnostics:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

If simulations of the same system without a ligand run fine, then the error is 
still related to the ligand, either its topology or placement.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
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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