I am having problems of protein stability (in a POPC membrane) during
equilibration and MD although the min heat density equil analyses imitated from
tutorial A3 were OK.
I suspect that the time-step 0.002 (see for example the in file below) is
giving the problems (Minimization was carried out without shake and heating
along the method of tutorial A3)
density equilibration
&cntrl
imin=0, irest=1, ntx=5,
nstlim=25000, dt=0.002,
cut=10, ntb=2, ntp=1, taup=1.0,
ntc=2, ntf=2,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntr=1,
restraintmask=":77-521 | :POP.O2, P1, O3, O4, O1, C15, C11, N, C12, C13, C14"
restraint_wt=32,
/
Before changing to dt=0.001, may I ask about updating non-bonded interactions,
which might also be relevant. As far as I understand from the manual of Amber9,
updating non-bonded interactions with a *.in file like above occurs by default
to security values. In descriptions from Amber8 non-bonded interactions were
set to be updated every 10 time steps. I would like to have this precise
condition. Much obliged for instructing me how to set that in Amber9.
francesco pietra
____________________________________________________________________________________
Be a better friend, newshound, and
know-it-all with Yahoo! Mobile. Try it now.
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Dec 16 2007 - 06:07:42 PST
