Re: Fixed atoms in SMD

From: khalil ghafarian (khalil_earth_at_yahoo.com)
Date: Tue Oct 09 2012 - 03:40:20 CDT

in PBC, I put empty space as a vacuum beside water box (in x direction), then in SMD section I applied external force in the same direction to my molecule. but as I said the whole water molecules move In X direction along with my molecule! Here is my config file: set temperature 298 # input coordinates input/output-inh-water.restart.coor extendedSystem input/output-inh-water.restart.xsc velocities input/output-inh-water.restart.vel structure input/inh-water.psf parameters input/inh-water.par paratypecharmm on # output set output output-SMD-inh-water outputname $output dcdfile ${output}.dcd xstFile ${output}.xst dcdfreq 1000 xstFreq 1000 binaryoutput no binaryrestart no outputEnergies 100 restartfreq 1000 # Basic dynamics exclude scaled1-4 1-4scaling 1 COMmotion no dielectric 1.0 # Simulation space partitioning switching on switchdist 10 cutoff 12 pairlistdist 14 #margin 2 # Multiple timestepping firsttimestep 0 timestep 1 stepspercycle 20 nonbondedFreq 2 fullElectFrequency 4 # Temperature control #temperature $temperature; # initial temperature # Langevin Dynamics langevin on; # do langevin dynamics langevinDamping 1; # damping coefficient (gamma) of 1/ps langevinTemp $temperature; # bath temperature langevinHydrogen no; # don't couple langevin bath to hydrogens seed 12345 # Pressure control langevinPiston off langevinPistonTarget 1.01325; # in bar -> 1.01325 bar = 1 atm langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp $temperature useFlexibleCell no useGroupPressure no fixedAtomsForces off # PBC #cellBasisVector1 200 0 0 #cellBasisVector2 0 30 0 #cellBasisVector3 0 0 30 wrapAll on dcdUnitCell yes PME yes PMEGridSpacing 1.0 # SMD SECTION SMD on SMDFile input/inh-water.ref SMDk 50 SMDVel 0.000005 SMDDir 1 0 0 SMDOutputFreq 100 # Scripting run 9000000 ________________________________ From: Axel Kohlmeyer <akohlmey_at_gmail.com> To: khalil ghafarian <khalil_earth_at_yahoo.com>; "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> Sent: Monday, October 8, 2012 3:30 PM Subject: Re: namd-l: Fixed atoms in SMD How should it be possible to pull a molecule out of the water, when you have periodic boundaries? -- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. ________________________________ From: khalil ghafarian <khalil_earth_at_yahoo.com> Sender: owner-namd-l_at_ks.uiuc.edu Date: Mon, 8 Oct 2012 03:22:25 -0700 (PDT) To: namd-l_at_ks.uiuc.edu<namd-l_at_ks.uiuc.edu> ReplyTo: khalil ghafarian <khalil_earth_at_yahoo.com> Subject: namd-l: Fixed atoms in SMD Hi, I want to pull out a molecule from water box with SMD,  but when I implemented  SMD ,I see the whole water box move with my molecule too , how can I keep water box fixed ? I have used PBC  and I specified SMD atoms exactly in reference file.

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