Re: Temperature during membrane equilibration

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Fri Sep 09 2011 - 11:17:53 CDT

Hola Andrés,

It doesn't look like you have anything in your input (config) file to
specify constant temperature. "langevinPistonTemp" only affects the
"dynamics" of the constant-pressure "piston", but won't serve to hold your
system temperature at any particular value. So the overall energy content
in your system, at the end of your heating run, must have been such that
once you began free dynamics, the system temperature settled at around 320
and stayed there.

In other words, you need to use "langevinTemp" (or one of the other
constant-temperature parameters) in your input file for production dynamics,
in order to actually have constant temperature at the desired value.

Erik

On Thu, Sep 8, 2011 at 7:33 PM, Andres Morales N <
andresmoralesn2_at_hotmail.com> wrote:

> hi
>
> I heated the system before equilibration. So I gave the velocities input
> (binvelocities dppc_cal300_1.vel) instead of temperature setting. I
> increased the temperature linearly from 0K to 300K using:
>
> temperature 0
> reassignFreq 25
> reassignIncr 0.375
> reassignHold 300
>
>
> I analized heating output and there was no problems. Temperature increase
> almost linearly from 0K to 300K
>
>
> ------------------------------
>
> Date: Thu, 8 Sep 2011 11:26:24 +0530
> Subject: Re: namd-l: Temperature during membrane equilibration
> From: ksubbu85_at_gmail.com
> To: andresmoralesn2_at_hotmail.com
>
> hi Andres Morales N
>
> where are you giving the temperature(means heating) in your input file.
> is it is ur complete input file.
>
> On Thu, Sep 8, 2011 at 10:27 AM, Andres Morales N <
> andresmoralesn2_at_hotmail.com> wrote:
>
> Dear NAMD Users:
>
> I performed a molecular dynamics simulation of a DPPC lipid bilayer with
> water. There was no errors during the process, that is during minimization
> (20000 steps), heating to 300 K (20000 steps) and equilibration (2 ns). I
> did no use 'restrains' in the system. The ensemble used was NPT with the
> protocol:
>
> #############################################################
> structure dppc_1.psf
> coordinates dppc_1.pdb
> bincoordinates dppc_cal300_1.coor
> binvelocities dppc_cal300_1.vel
> set outputname dppc_eq1ns_1
> firsttimestep 0
>
> paraTypeCharmm on
> parameters par_lipid27.rtf
>
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 8.
> pairlistdist 13.5
> margin 2.5
>
> timestep 1.0
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
> PME yes
> PMEGridSizeX 72
> PMEGridSizeY 72
> PMEGridSizeZ 96
>
> useGroupPressure yes
> useFlexibleCell no
> useConstantArea no
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp 300
>
> outputName $outputname
> dcdfreq 1000
> outputEnergies 100
>
> extendedSystem dppc_cal300_1.xsc
> wrapWater on
> wrapAll on
> wrapNearest off
>
> run 2000000
> #############################################################
>
> I expected system temperature fluctuates around 300 K, but when I analized
> the output file, I found that during the equilibration the temperature
> spikes from 300K to ~320K, by the second step, and then fluctuates around
> 320 K.
>
> Is it normal? Does anybody know how I could solve it?
>
> Thanks for your suggestions
>
>
> Hernán Andrés Morales Navarrete
>
> Biophysics and Molecular Modeling Group
> Physics Department
> Escuela Politécnica Nacional, Quito - Ecuador
> Ladrón de Guevara E11-253.
> Casilla 17-01-1253
> http://www.ciencias.epn.edu.ec/~biomod/
>
>
>
>
>
>

-- 
C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

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