RE: Problems restarting an amber simulation

From: Irene Newhouse (
Date: Wed Jan 16 2008 - 12:34:41 CST

While I haven't tried to switch a simulation between AMBER & NAMD - in fact, I'm not sure that that's such a hot idea - it complicates reproducibility - I have run both AMBER-style & CHARMM-style simulations with NAMD. I find that AMBER-style simulations are a lot less stable, and require more complex equilibration before they will run. One of the biggest bug-bears is trying to get away with a 2fs time step. I suggest you drop to 1, adjust the frequency of writing output so that you maintain your previous time interval per frame, & try again.
Irene Newhouse

Date: Wed, 16 Jan 2008 12:04:14 -0500From: sethl_at_gatech.eduTo: namd-l_at_ks.uiuc.eduSubject: namd-l: Problems restarting an amber simulationDear NAMD users,I have a simulation that was stable under AMBER 8 and wanted to restart it using NAMD. I assigned the Cell Basis Vectors according to page 13 of the GROMACS 3.3 manual. I am relatively new to NAMD and am not sure why I am getting the error below. I have also experimented with the margin size and get the same result.ERROR: Constraint failure in RATTLE algorithm for atom 246!ERROR: Constraint failure; simulation has become unstable.ERROR: Constraint failure in RATTLE algorithm for atom 5!ERROR: Constraint failure; simulation has become unstable.ERROR: Constraint failure in RATTLE algorithm for atom 61!ERROR: Constraint failure; simulation has become unstable.FATAL ERROR: Periodic cell has become too small for original patch grid!-------------------------------------------------------------------------------------------------------------------------------------My config file is as follows:rigidTolerance 0.0005 # Default is 0.00001numsteps 5000 # Num of total stepsoutputEnergies 50 # Energy output frequencyrestartfreq 1000 # Restart file frequencyDCDfreq 100 # Trajectory file frequencytimestep 2 # in unit of fstemperature 300 # Initial temp for velocity assignmentcutoff 10switching off # Turn off the switching functionsPME on # Use PME for electrostatic calculation# Orthogonal periodic box sizecellBasisVector1 66.119 22.040 -22.040cellBasisVector2 0 7.666 3.833cellBasisVector3 0 0 6.639cellOrigin 29.845 29.562 29.864PMEGridSizeX 70PMEGridSizeY 70PMEGridSizeZ 70amber on # Specify this is AMBER force fieldparmfile telomere-aza3-wat.prmtop # Input PARM fileambercoor md1.rst # Input coordinate fileoutputname test-10ps # Prefix of output filesexclude scaled1-41-4scaling 0.833333 # =1/1.2, default is 1.0Thank you for your help,Seth
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