Hello, I am following the tutorial A9 available at
http://ambermd.org/tutorials/advanced/tutorial9/ . I was able to
successfully complete the Step 1 (Removing charges) but while performing
step 2 i am facing the problem of
>> Coordinate resetting (SHAKE) cannot be accomplished,
>> deviation is too large
I reduced the time step to 0.001 but still the problem persists.
Is there any thing more to be added to the input file
My Infile is as follows
Process V0
PRM file: t4_bnz.prm
COMMENT
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 2500, ntwr = 10000, ntwx = 0,
ntf = 1, ntc = 2,
ntb = 2, cut = 9.0,
nstlim = 25000, dt = 0.001,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
icfe=1, clambda=0.1, ifsc=1, crgmask=':BNZ.H6', scmask=':BNZ.H6',
&end
Process V1
PRM file: t4_phn.prm
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 2500, ntwr = 10000, ntwx = 0,
ntf = 1, ntc = 2,
ntb = 2, cut = 9.0,
nstlim = 25000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
icfe=1, clambda=0.1, ifsc=1, crgmask=':PHN.O1,H6', scmask=':PHN.O1,H6',
&end
Thanks & Regards,
Shruti
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Received on Tue Mar 19 2013 - 05:00:02 PDT
