Dear all,
I have a problme with SHAKE after minimization, when I started to run md,
this is the error message i got:
------------------------------------------------------------------------------------------------------------------
Coordinate resetting (SHAKE) was not accomplished
within 3000 iterations
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
----------------------------------------------------------------------------------------------------------------
And the following are the scripts i used to run minimization and md:
--------------------------------------------------------------------------------------------------------------
initial minimisation whole system
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2000,
ntb = 1,
ntr = 0,
cut = 10
/
--------------------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------------------
res on the protein with 0.5fs timestep
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 30000, dt = 0.0005,
ntpr = 100, ntwx = 100, ntwr = 500
/
Keep the protein fixed with weak restraints
10.0
RES 1 791
END
END
---------------------------------------------------------------------------------------------------------------------
I have tried to use even smaller timestep such as 0.3fs or even 0.1fs, but
still i had same problem, and when i used very small timestep such as 0.1fs,
i will have error messages ' vlimit exceeded for step 1 ; vmax =
76.6082699232639' as well before it complained about the SHAKE problem.
Can anyone suggest what might be the causes of this SHAKE failure please?
thanks a lot in advance!
Best regards,
Rachel
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Received on Wed Nov 22 2006 - 23:01:47 PST
