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

Sanjay Kumar Upadhyay sanjay23 at iitb.ac.in
Fri Feb 11 05:47:51 CET 2011

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.

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
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
natural interaction in compare to other docked structures???

 Sanjay Kumar Upadhyay
 Research Scholor
 Protein Dynamics lab
 Dept of Chemistry
 IIT Powai, Mumbai, 400076
 Ph no. 09920200345, 09699353562,

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