Re: water box deformation

From: felmerino_at_uchile.cl
Date: Wed Feb 09 2011 - 12:57:23 CST

hey,

Since you are starting from a minimization all your atoms have no velocity. Your conf file is basically telling namd to start the dynamics (by the way, minimization uses no time sice it is just a conformational search) at 0K. Depending on how long your system reaches 310 K you could see some bubbles in the box. Indeed, even if you start at 310 K, if the box is bigger than the volume needed for the correct density you should see something like that.

 

Try to heat slowly your system using the reaasing freq command or reassigning the langevin temp variable.

 

 
----Mensaje original----De: ais_at_fh.huji.ac.ilFecha: 09-feb-2011 12:47Para: <namd-l_at_ks.uiuc.edu>Asunto: namd-l: water box deformationhi,i'm running an npt simulation with periodic boundary conditions.i notice that as the simulation advances, the water box collapses into a shape similar to a sphere.the current run is a restart over a 40ps minimization that i ran earlier on the system.in the minimization script i specified the periodic cell dimensions but in the restart run i didn't since i gave a restart xsc file.- could anyone suggest an explanation for this phenomenon &amp; point out what i've done wrong?- could this be related to the 'periodic cell has become too small for original patch grid...' error message that i get?i attach my restart conf file below. thanks, Ai############################################################### JOB DESCRIPTION ############################################################################################################################## ADJUSTABLE PARAMETERS ###############################################################structure 02_04_1zgoa_ion.psfcoordinates 02_04_1zgoa_ion.pdboutputName 10_1zgoaset temperature 310# Continuing a job from the restart filesif {1} {set inputname 07_1zgoabinCoordinates $inputname.restart.coorbinVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this!extendedSystem $inputname.xsc}firsttimestep 40000############################################################### SIMULATION PARAMETERS ################################################################ InputparaTypeCharmm onparameters par_all27_prot_lipid_ai.inp# NOTE: Do not set the initial velocity temperature if you# have also specified a .vel restart file!# temperature $temperature # Periodic Boundary conditions# NOTE: Do not set the periodic cell basis if you have also# specified an .xsc restart file!if {0} {cellBasisVector1 82.67 0. 0.cellBasisVector2 0. 88.12 0.cellBasisVector3 0. 0 92.44cellOrigin 19.00 -14.80 38.19}wrapWater onwrapAll on# Force-Field Parametersexclude scaled1-41-4scaling 1.0cutoff 12.switching onswitchdist 10.pairlistdist 13.5# Integrator Parameterstimestep 1.0 ;# 1fs/steprigidBonds all ;# needed for 2fs stepsnonbondedFreq 1fullElectFrequency 2 stepspercycle 10#PME (for full-system periodic electrostatics)if {1} {PME yesPMEGridSizeX 90PMEGridSizeY 90PMEGridSizeZ 96}# Constant Temperature Controllangevin on ;# do langevin dynamicslangevinDamping 5 ;# damping coefficient (gamma) of 5/pslangevinTemp $temperaturelangevinHydrogen no ;# don't couple langevin bath to hydrogens# Constant Pressure Control (variable volume)if {1} {useGroupPressure yes ;# needed for 2fs stepsuseFlexibleCell no ;# no for water box, yes for membraneuseConstantArea no ;# no for water box, yes for membranelangevinPiston onlangevinPistonTarget 1.01325 ;# in bar -> 1 atmlangevinPistonPeriod 200.langevinPistonDecay 50.langevinPistonTemp $temperature}restartfreq 500 ;# 500steps = every 1psdcdfreq 500xstFreq 500outputEnergies 100outputPressure 100# Fixed Atoms Constraint (set PDB beta-column to 1)if {0} {fixedAtoms onfixedAtomsFile myfixedatoms.pdbfixedAtomsCol B}# IMD Settings (can view sim in VMD)if {0} {IMDon onIMDport 3000 ;# port number (enter it in VMD)IMDfreq 1 ;# send every 1 frameIMDwait no ;# wait for VMD to connect before running?}############################################################### EXTRA PARAMETERS ################################################################ Put here any custom parameters that are specific to# this job (e.g., SMD, TclForces, etc...)############################################################### EXECUTION SCRIPT ################################################################ Minimizationif {0} {minimize 40000 ;#40 psreinitvels $temperature}run 1000000 ;# 1000ps=1ns

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