Dear Amber users,
I would like to know the limits of targeted molecular dynamics. I have generated a pathway for an RNA molecule that consists of several intermediate structures. When I go from one structure to another that has an all-atom RMSD of 2.5 angstroms it converges to the reference structure with little perturbations. When I change calculation so that the structure goes to another reference structure that has a higher all-atom RMSD, say 8 angstroms, it does converge to the appropriate structure, but when I plot the RMS from the first structure in Ptraj I get an oscillatory damping behavior (similar to an underdamped mechanical system). I am using pretty small force constants tgtmdfrc=0.01 to tgtmdfrc=0.1 (I have tried higher values but it doesn't change the results) and have the tgtfitmask and tgtrmsmask set to include only the backbone. So now to my questions. First, if 8 Angstroms is too high of an RMSD, what is considered a reasonable maximum value? Second, what causes the oscil!
lations,
I have tried multiple variations of tgtmdfrc, tgtmdrms, and RMSD values between intermediate structures and still get this pattern. Little is written on how the forces generated from targeted MD are weighted in with the other forces used to create a trajectory. Since the molecule does converge to the correct structure, is this oscillatory behavior considered to be okay? Please help me understand the basics of targeted MD. Below is a sample input code.
Thanks
Whitney
cat <<eof > mdin
equilibrate the structure
&cntrl
imin=0, ntx=5,
irest=1, ntxo=1,cut=15.0, tempi=300.0,
ntpr=100, ntwx=100, ntwe=1000,
nstlim=2000000,tautp=2, temp0=300.0,
dt=0.001, nscm=100,
igb=1,ntb=0, saltcon=0.5, gbsa=1,
ntt=1, nsnb=20,offset=0.13,
itgtmd=1, tgtrmsd=0.5, tgtmdfrc=0.01,
tgtfitmask=":1-76.P,O1P,O2P,O5',O4',O3',O2',C5',C4',C3',C2',C1'",
tgtrmsmask=":1-76.P,O1P,O2P,O5',O4',O3',O2',C5',C4',C3',C2',C1'",
&end
Group for target
RES 1 76
END
END
eof
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Received on Wed Nov 30 2005 - 16:53:01 PST
