On 7/6/12 1:12 AM, James Starlight wrote:
Dear Gromacs users!
I have some problems with the simulation of protein-ligand complex
embedded in the ccl4-water environment. In addition there are some
crystallography waters (xw) embedded in the protein interiour of the
protein. I've done equilibration and minimisation of my system and run
it in NVT ensemble.
Finally I've already simulated this system in the apo form as well as
without XW and there were no any problems.
In the current case my system always crashed after 10-15 ns of
simulation with the errors like
Step 6651310, time 13302.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.060675, max 1.520945 (between atoms 3132 and 3130)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3148 3147 90.0 0.1281 0.1483 0.1000
3150 3149 90.0 0.1084 0.1444 0.1000
3131 3130 90.0 0.1321 0.1325 0.1000
3132 3130 90.0 0.1067 0.2521 0.1000
-------------------------------------------------------
Program mdrun_mpi.openmpi, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/constr.c, line: 189
here both atoms 3132 and 3130 are from LIGAND.
During data analysing I didnt observed any serious artifacts in that
system. In addition RMSD both of protein and ligand were very stable.
Finally there are no fluctuations in energy or temperature. So I could
understand why this crasshes could occur. If I try to continue this
simulation from the crasshed checkpoint my simulation always goon but
within next 5-10ns I've always obtain second crash etc.
This is the last step from log file
DD step 6649999 vol min/aver 0.758 load imb.: force 1.0% pme
mesh/force 0.708
Step Time Lambda
6650000 13300.00000 0.00000
Energies (kJ/mol)
Angle G96Angle Proper Dih. Improper Dih. LJ-14
5.78299e+01 1.24988e+04 2.10966e+03 1.81619e+03 8.94229e+01
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
4.65481e+04 8.27301e+04 -6.89535e+03 -2.15286e+03 -7.16722e+05
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
-1.72813e+05 -7.52733e+05 1.46708e+05 -6.06025e+05 -1.37045e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.10968e+02 -9.74796e+01 2.52993e+02 1.55693e-05
Could you explain me what could be wrong with that system and what
addition data should I provide to help sheld light on that problem ?
If the addition of a ligand causes the simulation to crash (and the simulation
runs normally in the apo form with and without crystal waters), then that sounds
like a problem with the ligand topology or its initial placement.
What is the ligand? How did you generate and validate its topology? How did
you place it?
-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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