Dear Ambers,
I am working on a hetero protein dimer, and following the first MD heating stage, there is a slight shift of the position of one monomer with respect to the other, about 0.5 Ang, in fact the center of mass shifts in a single frame 0.8Ang at the end of the system heating equilibration, with the protein restrained. The following stage is a constant pressure equilibration as seen bellow. I dont’ see this jump of monomer a versus b again during the simulation. It happens only once. I have seen this in another system, although the subsequent analysis etc seems just fine.
I don’t understand why I see it, and if this is a visualization issue? or a real problem?, am I doing something wrong? Why does it happen? How I can check it?
Thanks!
1) heating
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 0, ntx = 1, ig = -1,
tempi = 100.0, temp0 = 298.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 1,
ntt =3, gamma_ln=1., ntb = 1, ntp = 0,
nscm = 0,
ntr=1, restraintmask="!:WAT & !.H=", restraint_wt=100.0 nmropt=1,
ioutfm=1, ntxo=2,
/ &wt
TYPE="TEMP0", istep1=0, istep2=1000000,
value1=100., value2=298., /
&wt TYPE="END",
/ /
2) equilibration constant pressure
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
temp0 = 298.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 1, taup = 0.1,
ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1,
nscm = 0,
ntr=1, restraintmask="!:WAT & !.H=", restraint_wt=100. ioutfm=1, ntxo=2,
/
Best,
Fabian
Fabian Glaser PhD
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
http://bku.technion.ac.il/
Tel +972 (0) 4 8293701
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Received on Wed Nov 06 2019 - 01:00:02 PST
