Dear users,
I have set up an SMD simulation to stretch an RNA helix. In this set up
file, i am increasing the distance between two atoms from an initial value
of 29 Ang to 50Ang. This is my config file:-
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
ntr = 1,
restraintmask ='.817',
restraint_wt = 20,
pres0 = 1,
ntp = 1,
taup = 2.0,
cut = 10.0,
ntc = 2,
ntf = 2,
tempi = 310.0,
temp0 = 310.0,
ntt = 3,
ig = -1,
ioutfm = 1,
iwrap = 1,
gamma_ln = 1.0,
nstlim = 2000000, dt = 0.002, tol = 0.00001,
ntpr = 1000, ntwx = 1000, ntwr = 50000,
jar = 1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist_rk2_3.RST
DUMPAVE=dist_vs_t_rk2_3_2
LISTIN=POUT
LIST=POUT
-------------------------------------------------
rst file-
#change distance between atoms 27 and 817
&rst iat=27,817, r2=29, rk2 = 3.0, r2a=50, /
-------------------------------------------------------
My problem is that when i am trying to restart the SMD from the final
conformation obtained from previous run, and extending from 50 to 71 Ang in
next run (after changing r2 and r2a in RST file), i am getting a drop in
force and work values to 0.00. Why is this happening. Isn't it supposed to
pick the final force and work values from previous runs??
The reason i am trying to run the simulation in steps is because i am not
sure of the final extension to which i need to extend the helix.
Thank you,
Asmita
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Received on Sat May 09 2015 - 08:00:03 PDT
