[AMBER] Equilibration problem large system in explicit solvent

From: Waldner, Birgit <Birgit.Waldner.uibk.ac.at>
Date: Wed, 7 Jan 2015 13:12:20 +0000

Dear Amber users,

I am trying to simulate a rather large system (tetramer) in explicit solvent (TIP3P 12 octahedral box) using pmemd.cuda.

After minimization, in my first NVT-equilibration step I keep the solute fixed (restraint_wt=1000.0) and slowly heat the system up from 100 to 300K. However, after this step, the equilibration crashes giving only the following error message:

ERROR: I could not understand line 94564
  -0.0863324 0.0579049 0.0266437 0.8450111 0.0988997 -0.5613073

When I look at the *.out file of the first equilibration step, I notice that TEMP(K)= NaN, Etot= NaN and the restraints exceed 2000 already after a few steps.

The *crd-file after the first equilibration step doesn't show diffusion of the monomer units building up the tetramer. Changing the parameters and heating up the system more slowly also doesn't help. I also tried using netcdf restart file format.

Has anyone encountered a similar problem and can point me in the right direction on how to fix this error? The equilibration of just the monomer using the same equilibration protocol works fine.

Thank you for your help, best regards,


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Received on Wed Jan 07 2015 - 05:30:05 PST
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