While carrying out a simulation on a DNA dodecamer with AMBER 5.0, using
PME I was faced with the problem of translation - rotation of the solute
in the solvent resulting in the migration of the DNA out of the "real"
water-box.
On the advice of one of my friends I modified my sander input (as below)
and that eliminated the translation but my DNA still rotates.
If there 's any solution to eliminate both translation and rotation
movement without over perturbating the system (as explained in "The Flying
Ice Cube: Velocity Rescaling in Molecular Dynamics Leads to Violation of
Energy Equipartition "Journal of Computational Chemistry 1998 )
I will be very grateful to know it.
Simulation 1, 12mer, SANDER input
&cntrl
imin = 0, ntx = 7, ntpr = 250, ntwx = 500,
ntwe = 0,
ntcm = 1, nscm = 500, ndfmin = 6,
ntwxm = 0, ntwem = 0, ntwprt = 776,
ntf = 2,
ntb = 2, ntp = 1, pres0 = 1.0,
ntc = 2, nsnb = 10,
scee = 1.2, idiel = 1,
nrun = 20, nstlim =5000,
cut = 9.0,
t =0.0, dt =.002,
irest = 1, init = 4,
tempi = 0.0, temp0 =300., ntt = 5, dtemp = 4.,
isolvp = 754,
ig =10,
iewald = 1,
ntr = 0,
&end
66.0781 38.2139 42.5853 90.0 90.0 90.0
66 38 43 4 0 0 0
0.000001
Emmanuel Giudice
Laboratoire de Biochimie Theorique CNRS UPR 9080
Institut de Biologie Physico - Chimique
13, Rue Pierre & Marie CURIE 75005 PARIS
Tel : 01.58.41.51.68
Email : Emmanuel.Giudice_at_ibpc.fr
Received on Tue Jan 11 2000 - 06:19:31 PST
