Re: problems with temperature control

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Nov 03 2010 - 19:58:06 CDT

Hi Pegah,
Using a specific seed that is the same for subsequent simulations is a
Bad Idea, especially if you have short run segments. See
http://pubs.acs.org/doi/abs/10.1021/ct8002173?journalCode=jctcce and
related articles for why. This may lead to the unexpected correlations
that you're experiencing.

Best,
Peter

On 11/03/2010 05:28 AM, Pegah Khalili wrote:
> Dear All,
>
> I am new to NAMD and am having some problems with using a suitable
> temperature control algorithm for my system.
>
> My system involves heating, equilibrating and running dynamics on
> cyclodextrins in a waterbox with periodic boundary conditions, using the
> NPT ensemble. I am currently testing this for alpha-cyclodextrin.
>
> I have run equilibration (1ns) and dynamics (100ns) on
> alpha-cyclodextrin using Langevin dynamics for temperature and pressure
> control, but the temperature and energy fluctuations are high during the
> simulation (temp. fluctuates between 290-305K, and energy fluctuates
> between -32400 and -31800 kcal/mol - is this normal?).
>
> Also, the time correlation functions I generate using the 100ns
> simulations do not decay exponentially like they should - I think this
> is due to using the Langevin dynamics method for temperature control,
> but I am not sure.
>
> Would anyone be able to help me with this problem. Do I need to use a
> different method for temperature and pressure control? Is this causing
> problems with the correlation functions?
>
> Thank you in advance.
> I have included a copy of my dynamics input script below:
>
> set temperature 298.15
> #numsteps 100
> dielectric 1.0
> #firsttimestep 0
>
> if {1} {
> set inputname ACD_whed-1
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel
> extendedSystem $inputname.xsc
> }
>
> coordinates ACD_whed-1.coor
> outputname ACD_whed-2
> outputEnergies 100
> binaryoutput no
> DCDFreq 100
> restartFreq 100
> #temperature $temperature
>
> structure acd_water_heat_xpl.psf
> paraTypeCharmm on
> parameters par_all22_prot.inp-kjn-map
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 10.0
> cutoff 12.0
> pairlistdist 14.0
>
> seed 27041994 ;#seed value
> timestep 1.0 ;# 1fs/step
> rigidBonds all ;# needed for 2fs steps
> rigidTolerance 1.0E-10
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> if {0} {
> cellBasisVector1 49.8129 0. 0.
> cellBasisVector2 0. 49.8129 0.
> cellBasisVector3 0. 0. 49.8129
> cellOrigin -0.0207 -0.0727 -0.0403
> }
> wrapWater on
> wrapAll on
>
> if {1} {
> PME yes
> PMEInterpOrder 6 ;# interpolation for B-spline
> PMEGridSizeX 54
> PMEGridSizeY 54
> PMEGridSizeZ 54
> PMETolerance 4.6809305e-9 ;# corresponds to a KAPPA value of 0.32
> }
>
> if {1} {
> useGroupPressure yes
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
> #minimize 1000
> #reinitvels $temperature
>
> run 500000 ;# 500ps

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:43 CST