From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Thu Sep 08 2011 - 18:33:47 CDT
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/
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