From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Mon Aug 20 2007 - 05:20:06 CDT
Hi,
I have a solvated TM protein membrane simulation system of ~ 80000 atoms.
After about 40 ns of simulation, the protein-membrane complex drifts in the
-z direction (along the bilayer normal) by about 7-8 Angstroms. The bulk
solvent, however, drifts in the opposite direction by approximately the same
distance. The overall center of mass does not drift. Please see the attached
graph for the center of mass progression of the different components,
>From my naive knowledge, systematic drift is common in simulations, and can
be corrected by recentering and reorienting the trajectory after the
production runs. But is it possible to have drift of different components of
a simulation in different directions ? Is something wrong in the simulation
?
I have used SHAKE with a timestep of 2fs (SHAKE was applied to all hydrogen
atoms). Electrostatics and vdw energies are calculated every step. All the
other parameters are typical. The config file is at the end of the email.
Thank you for the help,
-Maria
-- Maria G. Technical University of Denmark Copenhagen ----------------------------------------------------------- # NAMDConfiguration file set pmex 125 set pmey 125 set pmez 100 ## .. read structure and parameters here set temp 310 outputEnergies 5000 outputTiming 5000 outputPressure 5000 xstFreq 5000 dcdFreq 5000 wrapAll on rigidbonds all timestep 2 nonBondedFreq 1 fullElectFrequency 1 stepsPerCycle 20 exclude scaled1-4 1-4scaling 1.0 switching on switchDist 10 cutoff 12 pairlistdist 14 Pme on PmeGridsizeX $pmex PmeGridsizeY $pmey PmeGridsizeZ $pmez ######################################### # PRESSURE AND TEMPERATURE CONTRON ######################################### # temperature langevin on langevinDamping 5 langevinTemp $temp langevinHydrogen no useflexiblecell yes langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 100 langevinPistonDecay 50 langevinPistonTemp $temp binaryoutput on outputname system-1 run 100000
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:07 CST