From: Kang Hee Cho (gkdkang_at_gmail.com)
Date: Thu Jan 20 2011 - 21:25:46 CST
Hi, everyone.
I am trying to simulate a protein using NAMD, but I am having a
problem with discrete energy value.
I want to simulate protein with NAMD 3 steps.
First, minimization. (all atoms are fixed except backbone)
Second, minimization with the backbone of the protein fixed.
Third, execution with the backbone fixed.
I restarted my protein but I found that the energy of the last step of
the first minimization and the starting step of the second one is
different.
Last step of first minimization
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL
TOTAL3 TEMPAVG
ENERGY: 1000 58.4236 481.1728 286.8849 4.8477 -2588.3444 -91.7916
0.0000 0.0000 0.0000 -1848.8071 0.0000 -1848.8071 -1848.8071 0.0000
Starting step of second simulation
ENERGY: 1000 237.1904 2565.7394 553.0368 0.6446 -4628.9693 6496.4700
0.0000 0.0000 0.0000 5224.1119 0.0000 5224.1119 5224.1119 0.0000
I have tried a lot of things, but I don't know what to do.
Any help would be appreciated.
Cho
The molecule “qsu.psf”, “qsu.pdb” were used in the simulation.
The file “qsu_nw_eq.conf” was written for the first step and the file
“qsu_nw_eq2.conf” was for the second step
Another question is why I have to minimize whenever fixed atoms change
their position?
------------------------------------------
"qsu_nw_eq.conf"
structure qsu.psf
coordinates qsu.pdb
set temperature 300
set outputname qsu_nw_eq
firsttimestep 0
# Input
paraTypeCharmm on
parameters par_all22_prot.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 13.5
switching on
switchdist 10.
pairlistdist 16.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 50
outputEnergies 100
outputPressure 100
# Fixed Atoms Constraint
fixedAtoms on
fixedAtomsFile qsu_nw_eq.ref ;# all atoms are fixed except backbone
fixedAtomsCol B
# Minimization
minimize 1000
--------------------------------------
"qsu_nw_eq2.conf"
structure qsu.psf
coordinates qsu.pdb
bincoordinates qsu_nw_eq.coor
binvelocities qsu_nw_eq.vel
#extendedSystem
set outputname qsu_nw_eq2
firsttimestep 1000
# Input
paraTypeCharmm on
parameters par_all22_prot.inp
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 13.5
switching on
switchdist 10.
pairlistdist 16.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 50
outputEnergies 100
outputPressure 100
# Fixed Atoms Constraint
fixedAtoms on
fixedAtomsFile qsu_nw_eq2.ref ;# backbone of the protein fixed
fixedAtomsCol B
# Minimization
minimize 1000
run 1000
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