MD-problems-GPCR in POPC bilayer

From: jose correa (corrjose_at_gmail.com)
Date: Tue Nov 25 2008 - 09:30:50 CST

Dear NAMD users

I have problems with a GPCR inbedded in POPC bylayer membrane, once
that all system was built, it was solvated. Then, the water were
minimized freeze the backbone protein. This is ok, however, when I try
to run short MD to the same system the program yield this problem and
stop the simulation:

Info: Entering startup phase 6 with 53896 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 53896 kB of memory in use.
Info: CREATING 5476 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.3715e-16 AT 0.200098
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 9.86316e-17 AT 0.220971
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 3.70577e-22 AT 9.99687
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.12849e-16 AT 9.94673
Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 1.05879e-22 AT 9.99687
Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 4.47524e-17 AT 9.99687
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.05879e-22 AT 9.94673
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 2.93092e-16 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 3.9443e-31 AT 9.89634
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.37662e-14 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.97215e-31 AT 9.94673
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 6.7893e-16 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 10.0468
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 1.12482e-14 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.61892e-25 AT 9.94673
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 1.24935e-15 AT 9.94673
Info: Entering startup phase 8 with 58852 kB of memory in use.
Info: Finished startup with 86652 kB of memory in use.
TCL: Running for 15000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 2370!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 6776!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 9.458918 CPUTime: 8.650000 Memory: 179316 kB
Program finished.

Can somobody give me any suggestion?
Best wishes
Jose Correa-Basurto

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