From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Thu Jun 26 2008 - 02:46:41 CDT
Hi Jawahar,
There are only a limited number of settings that can be altered on the fly in the configuration file and FEP is not one of them - but you should be able to achieve the result you want by actviating FEP from the beginning of the run, with lambda set to 0.5.
Best regards,
Floris Buelens
----- Original Message ----
From: Jawahar Neelankatan <neelankatan_j_at_yahoo.com>
To: namd-l_at_ks.uiuc.edu
Sent: Wednesday, 25 June, 2008 2:28:21 AM
Subject: namd-l: Running minimization, heating and FEP simulation within the same configuration file.
Hi all,
I am interested in doing an FEP simulation that involves mutation of one amino acid in a protein to another.
I have solvated the protein system and I would like to minimize it, heat it up slowly, equilibrate it for about 200 ps, and then run FEP calculations (in NPT ensemble) with the 200ps-equilibrated system used as a starting point. I'm trying to do all this in one configuration file but I'm getting a strange error. I am able to do the minimization, heating and equilibration, but as soon as it gets to the FEP stage, it crashes with the following error:
TCL: Setting parameter fep to on
FATAL ERROR: Setting parameter fep from script failed!
FATAL ERROR: Setting parameter fep from script failed!
FATAL ERROR: Setting parameter fep from script failed!
FATAL ERROR: Setting parameter fep from script failed!
FATAL ERROR: Setting parameter fep from script failed!
FATAL ERROR: Setting parameter fep from script failed!
FATAL ERROR: Setting parameter fep from script failed!
FATAL ERROR: Setting parameter fep from script failed!
The error message gives no clue as to why the crash occurred, other than repeatedly announcing that it did. If anyone has done FEP calculations before, could you please tell me how to do a minimization, heating, equilibration and FEP calculation (in NPT ensemble) all in one configuration file ?
I have attached to this email a copy of the configuration file I used, I also posted it below. Thanks.
-Jawahar
#------------------CONFIG FILE-----------
structure /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/colicin/struct/1prw_solv.psf
coordinates /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/colicin/struct/1prw_solv.pdb
bincoordinates /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/colicin/struct/1prw_solv.coor
set output prwsolv_min+heat+eq+FEP_run1
#
cellBasisVector1 74.508 0.0 0.0
cellBasisVector2 0.00 78.016 0.0
cellBasisVector3 0.00 0.00 172.903
cellOrigin 0.605 -0.769 0.056
# forcefield information
paratypecharmm on
parameters /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/CHARMMPARAMS.prm
exclude scaled1-4
1-4scaling 1.0
rigidBonds water
wrapWater on
wrapAll on
#
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 13.5
#margin 2.5
stepspercycle 20
nonbondedFreq 1
timestep 2.0 ;# 2fs/step
#
PME on
PMEGridSizeX 75
PMEGridSizeY 75
PMEGridSizeZ 180
fullElectFrequency 4
outputname $output
restartfreq 500
dcdfreq 100
xstFreq 100
outputEnergies 500
outputPressure 500
set temperature 50
temperature $temperature
set dstep 50
useGroupPressure yes
langevin on
langevinDamping 1.0
langevinHydrogen off
BerendsenPressure on
BerendsenPressureTarget 1.01325
BerendsenPressureCompressibility 4.57E-5
BerendsenPressureRelaxationTime 100
BerendsenPressureFreq 4
minimize 20000
firsttimestep 0
# script for heating the system up to desired temperature
while { $temperature < 301 } {
langevinTemp $temperature
if {$temperature == 300} {
firsttimestep 0
run 200000
} else {
run 40000
}
set temperature [expr $temperature + $dstep]
}
# FEP PARAMETERS
source fep.tcl
fep on
fepFile 1prw_solv.fep
fepCol B
fepOutFile prwsolv_min+heat+eq+FEP_run1.fepout
fepOutFreq 10
fepEquilSteps 200000
set nSteps 2000000
set dLambda 0.1
set init { 0.02 0.1 }
set end { 0.9 0.98 }
runFEPlist $init $nSteps
runFEP 0.1 0.9 $dLambda $nSteps
runFEPlist $end $nSteps
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