ABF:restraint in free energy calculation in Zcoord-method

From: (supram_at_nankai.edu.cn)
Date: Tue Feb 03 2009 - 22:15:42 CST

Dear Namd developers,

       I am running a free energy calculation with ABF method for the complex of -CD
with L-glutamic acid (Glu) in waters. The abf coordinate is zCoord. When running the free energy calculation, I "fixed"the abf abf1 { 14 35 56 77 98 119 140 }glycosidic oxygen atoms center at the origin coordinate(O cooridinate); and I "constraint" the abf abf2 { 149 150 164 165 } carboxylic oxygen atoms of the L-glutamic acid on the XY plan to make sure the L-glutamic acid (Glu) moves along the Z axis(if I don't do so, the L-glutamic acid did not move along the the Z axis).
 
     Is my method reasonable? if the method affects free energy calculation,is there other better methods to make sure that the L-glutamic acid (Glu)moving along the Z axis and don't affect the free energy calculation?

     I will be very deeply grateful for your any help, thank you very much!!!!!!!(i)
     Here are my config file for the ABF simulation.

structure bcdlglu_wb_na.psf
coordinates restart.coor
velocities restart.vel
extendedsystem restart.xsc
firsttimestep 1010000

paraTypeCharmm on
parameters par_all22_prot.inp
parameters CSFF_parm.inp

exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 12.0
pairlistdist 16.0

timestep 1.0
rigidbonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

langevin on
langevinDamping 1
langevinTemp 298.15
langevinHydrogen on

useGroupPressure yes
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 298.15

wrapwater on
wrapall on

PME on
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 60

fixedatoms on
fixedatomsfile bcdlglu_wb_na_f.pdb
fixedatomscol B

constraints on
consref restart.coor
conskfile bcdlglu_wb_na_h.pdb
conskcol B
selectconstraints on
selectconstrx on
selectconstry on
selectconstrz off

outputName output-ABF
binaryoutput no
outputEnergies 1000
outputTiming 1000
outputPressure 1000
dcdfile bcdlglu_wb.dcd
dcdfreq 1000
dcdunitcell yes
xstfreq 1000
restartname restart-1
binaryrestart no
restartfreq 1000

source /nfs/s09r2p2/yuliu_nk/NAMD2.6-1/Abf/abf.tcl

abf coordinate zCoord

abf abf1 { 14 35 56 77 98 119 140 }

abf abf2 { 149 150 164 165 }

abf ximin -8
abf ximax -4
abf dxi 0.1

abf fullsamples 1000

abf dsmooth 0.1

abf forceconst 20
abf applybias yes

abf outputfreq 1000

abf writexifreq 1000

abf outfile bcdlglu.abf

run 4000000

z{Sʗ{٥r
z{S}ĝxjǺ<P>Dear Namd developers,<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I am running a free energy calculation with ABF method for the complex of -CD <BR>with L-glutamic acid (Glu) in waters. The abf coordinate is zCoord. When running the free energy calculation,&nbsp; I "fixed"the&nbsp;abf abf1 { 14 35 56 77 98 119 140 }glycosidic oxygen atoms center at the origin coordinate(O cooridinate); and I "constraint" the abf abf2 { 149 150 164 165 } carboxylic oxygen atoms of the L-glutamic acid on the XY plan to make sure the L-glutamic acid (Glu) moves&nbsp;along the Z axis(if I don't do so, the L-glutamic acid did not move along the the Z axis).<BR>&nbsp;<BR>&nbsp;&nbsp;&nbsp;&nbsp; Is my method reasonable? if the method&nbsp;affects free energy calculation,is there other better methods to make sure that the L-glutamic acid (Glu)moving&nbsp;along the Z axis and don't affect the&nbsp; free energy calculation?<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp; I will be very deeply grateful for your any help, thank you very much!!!!!!!(i) <BR>&nbsp;&nbsp;&nbsp;&nbsp; Here are my config file for the ABF simulation.<BR><BR>structure bcdlglu_wb_na.psf <BR>coordinates restart.coor <BR>velocities restart.vel <BR>extendedsystem restart.xsc <BR>firsttimestep 1010000 <BR></P>
<P>paraTypeCharmm on <BR>parameters par_all22_prot.inp <BR>parameters CSFF_parm.inp <BR>
<P>exclude scaled1-4 <BR>1-4scaling 1.0 <BR>cutoff 14.0 <BR>switching on <BR>switchdist 12.0 <BR>pairlistdist 16.0 <BR>
<P>timestep 1.0 <BR>rigidbonds all <BR>nonbondedFreq 1 <BR>fullElectFrequency 2 <BR>stepspercycle 20 <BR>
<P>langevin on <BR>langevinDamping 1 <BR>langevinTemp 298.15 <BR>langevinHydrogen on <BR>
<P>useGroupPressure yes <BR>useFlexibleCell no <BR>useConstantArea no <BR>
<P>langevinPiston on <BR>langevinPistonTarget 1 <BR>langevinPistonPeriod 100 <BR>langevinPistonDecay 50 <BR>langevinPistonTemp 298.15 <BR>
<P>wrapwater on <BR>wrapall on <BR>
<P>PME on <BR>PMEGridSizeX 36 <BR>PMEGridSizeY 36 <BR>PMEGridSizeZ 60 <BR>
<P>fixedatoms on <BR>fixedatomsfile bcdlglu_wb_na_f.pdb <BR>fixedatomscol B <BR>
<P>constraints on <BR>consref restart.coor <BR>conskfile bcdlglu_wb_na_h.pdb <BR>conskcol B <BR>selectconstraints on <BR>selectconstrx on <BR>selectconstry on <BR>selectconstrz off <BR>
<P>
<P>outputName output-ABF <BR>binaryoutput no <BR>outputEnergies 1000 <BR>outputTiming 1000 <BR>outputPressure 1000 <BR>dcdfile bcdlglu_wb.dcd <BR>dcdfreq 1000 <BR>dcdunitcell yes <BR>xstfreq 1000 <BR>restartname restart-1 <BR>binaryrestart no <BR>restartfreq 1000 <BR>
<P>source /nfs/s09r2p2/yuliu_nk/NAMD2.6-1/Abf/abf.tcl <BR>
<P>abf coordinate zCoord <BR>
<P>abf abf1 { 14 35 56 77 98 119 140 } <BR>
<P>abf abf2 { 149 150 164 165 } <BR>
<P>abf ximin -8
<P>abf ximax -4
<P>abf dxi 0.1 <BR>
<P>abf fullsamples 1000 <BR>
<P>abf dsmooth 0.1 <BR>
<P>abf forceconst 20
<P>abf applybias yes <BR>
<P>abf outputfreq 1000 <BR>
<P>abf writexifreq 1000 <BR>
<P>abf outfile bcdlglu.abf <BR>
<P>run 4000000 <BR></P>

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