From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Fri Sep 09 2011 - 20:57:36 CDT
Hi Erik
Thanks for your help. Your suggestion solved my problem.
Kind regards
Andres
Date: Fri, 9 Sep 2011 12:17:53 -0400
Subject: Re: namd-l: Temperature during membrane equilibration
From: nordgren_at_sas.upenn.edu
To: andresmoralesn2_at_hotmail.com
CC: namd-l_at_ks.uiuc.edu
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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