Dear Amber Users,
I am having trouble understanding how the RMSD is calculated in targetted
MD simulations. I have the following input file:
------------ tgtmd.in ------------------------
TMD: NMR->XRAY; target rmsd 3.267; resid 1-2,8-11,17-18 restrained
&cntrl
imin = 0, ntx = 5, nstlim = 1200000, irest=1,
dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
tempi = 300.0, temp0 = 300.0,
scee = 1.2, cut = 99.9,
ntpr = 50, ntwx = 50, ntwr = 50,
ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
igb = 1, nscm = 0, nmropt = 0,
ntr = 1, restraint_wt=0.02,
restraintmask=":1-2,8-11,17-18",
itgtmd = 1, tgtrmsd = 3.267, tgtmdfrc = 1.0,
tgtrmsmask="(:3-7,12-16)",
/
-----------------------------------
What this script does is it restraints the residues 1-2,8-11,17-18
with a restraint weight of 0.02. While doing that, implicitly, it aligns
the system with respect to restraintmask.
Then, the rmsd is calculated for the residues 3-7,12-16. At each
step, "Current RMSD from reference" is printed out. I could not figure out
how this 'Current RMSD from reference' is calculated. When I extract that
particular snapshot from the trajectory and use ptraj (first aligning the
residues 1-2,8-11,17-18 and then calculating the rmsd of residues
3-7,12-16), I get pretty different result.
1. Is there a mistake the way I describe/understand the above input file?
2. Does TMD follow a different alignment algorithm?
Thanks in advance for your responses.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
= Department of Chemistry - =
= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
= http://www.pas.rochester.edu/~yildirim/ =
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 23 2007 - 06:07:52 PDT
