Error in membrane protein simulation

Date: Sat Sep 01 2012 - 01:59:27 CDT

Dear all,
       I am trying to simulate a protein embedded in a POPC membrane. I am
following the NAMD tutorial on membrane proteins. When I go to the first
equilibration step using constraints mentioned in the step "melting of
membrane" I get "Constraints failure in rattle algorithm" with rigidbonds
all and "Atoms moving too fast" with rigidbonds water. I looked for the
solutions in mailing list and tried 1) decreasing time step to 0.5, 2)
increasing minimization steps from 1000 to 10000, 3) increasing
pairlistdist to 16, 4) setting margin upto 10, 5) gradually heating at a
slow rate. Also I noticed that during minimization I have energies
9999999. I have checked the atoms mentioned in the error file visually
and they are distributed throughout the membrane.There are more than 5000
of them. I made the membrane using VMD membrane plugin. Can someone
please tell me where I might be making an error.



सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
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दूरभाष/EPABX :0172 6665 201-202

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