[gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 11 06:59:07 CET 2011

On 11/02/2011 3:47 PM, Sanjay Kumar Upadhyay wrote:
> Dear gmx-users
> I am experiencing some problems running a protein-protein docked
> structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs.
> I have 20 docked (protein-protein) structures of one common protein with
> two different homologous protein, 10 from each group and started
> simulations for all, using same parameters.
> I did energy minimization for all the systems, all systems reached to
> energy minimized configuration in between 10000 to 12000 steps using steep
> algorithm and PE for all minimized systems are vary between -3975853 to
> -3571906 KJ/mol.
> In final MD out off 10 simulations 9 from each group was crassed in
> between 200 ps to 900 ps with lincs warning. However one simulation from
> each group running well up to 5 ns, and after 5ns out of these two, one
> simulation crassed with too many lincs warning, while other one completed
> 20ns and steel continue.

It sounds like you are not using a proper equilibration protocol before 
attempting to run MD. Occasionally that can work, but often it doesn't. 


> when restarting the *crashed *simulation feeding "-cpi md.cpt" to mdrun
> the simulation restarts fine with few steps before but stopped at same
> portion of the simulation with same lincs warning. I checked the energy
> and temperature distribution and find that potential energy is
> fine,however total energy of systems as well as temperature (300K attain
> 321K
> at last steps) is higher at last steps before simulation stops.I read
> all the mailing least before posting this question but did not reach any
> conclusion. Any explanation or solution for this, why one simulation is
> stable and running fine up to more than 20ns however others are crassed
> with same parameters?? I am thinking that it may be because of steric
> class between docked protein. Is it mean that one docked structure making
> more
> natural interaction in compare to other docked structures???
>   Regards
>   Sanjay Kumar Upadhyay
>   Research Scholor
>   Protein Dynamics lab
>   Dept of Chemistry
>   IIT Powai, Mumbai, 400076
>   Ph no. 09920200345, 09699353562,

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