Dear all,
I would like to simulate a DNA base flipping process using umbrella sampling and PMF.
I defined the center of mass of four groups and set the dihedral restraint of these center points during umbrella sampling.
However, the output dihedral angles by Sander are very different to those calculated by Ptraj using trajectory file. According to the MD trajectory, I thought there might be something wrong with the dihedral angles output by Sander, because the fluctuation of the dihedral angles were too big!
It was so weird that if I defined the dihedral angles by four real atoms instead of center of mass, the outputs by Sander and Ptraj were exactly the same!
How it happened £¿ And which output file of dihedral angles I should use in PMF calculation?
The namelist files for MD:
equilibration of the whole system
&cntrl
imin=0,irest=0,ntx=1,ig=-1,
nstlim=1000,dt=0.001,
ntc=1,ntf=1,
cut=8.0,ntb=2,ntp=1,taup=2.0,
ntt=3,gamma_ln=2.0,
temp0=300.0,tempi=300,
ntpr=1,ntwx=1,ntwr=1,
ntr=1, restraintmask='!(:CAC|.155,188,189,190,191)', restraint_wt=2.0,
nmropt=1
/
&wt type='DUMPFREQ', istep1=1 /
&wt type='END' /
DISANG=dih_35_IAT.RST
DUMPAVE=dih_35_IAT.out
the DISANG file:
&rst
iat=-1,-1,-1,-1, r1=-145, r2=35, r3=35, r4=215, rk2=100, rk3=100,
igr1=136,137,139,140,141,142,145,146,148,149,550,551,553,554,558,559,560,562,563, igr2=131,133,134,152,150, igr3=163,165,166,172,169, igr4=174,175,176,177,178,179,182,183,185,186,187 /
the ptraj script file:
trajin win_35.mdcrd
dihedral d1 .136,137,139,140,141,142,145,146,148,149,550,551,553,554,558,559,560,562,563 @131,133,134,152,150 @163,165,166,172,169 @174,175,176,177,178,179,182,183,185,186,187 out traj_dih35.out
the center of mass are defined by same atoms in DISANG file and ptraj scripts
Thank you!
From Junyan Lu
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Received on Mon Feb 06 2012 - 23:30:03 PST
