Dear Amber users,
I'm running targeted MD using Amber18 and this is my input file:
targeted MD tgtfitmask
&cntrl
imin = 0, ntx = 5, nstlim = 700000, irest = 1,
dt = 0.002, ntc = 2, ntf = 2,
temp0 = 300.0,
cut = 8.0,
ntpr = 2000, ntwx = 5000, ntwr = 10000,
ntb = 2, ntt = 3, ntp = 1,
igb = 0, nmropt = 1, gamma_ln = 2.0,
tgtfitmask = ":490,870,47,669,769,567,869,872,892,891,495,894,409,665,900,798,388,871,61,489,630,893,791,631,795,881,778,576,883,793,788,799,584,336,758,797,182,767,581,26,158,796,347,656,677,695,681,660,675,694,8,190,671,794,252,354,10.CA",
itgtmd = 1, tgtmdfrc = 20.0,
tgtrmsmask = ":940-967.P",
/
&wt
TYPE = 'TGTRMSD', istep1 = 1, istep2 = 500000,
value1 = 3.0, value2 = 0.0,
/
&wt
TYPE = 'TGTRMSD', istep1 = 500001, istep2 = 700000,
value1 = 0.0, value2 = 0.0,
/
&wt
type = "END",
/
I changed the 'tgtmdfrc' in the input file, and when tgtmdfrc=100 there came the error "coordinate resetting (SHAKE) cannot be accomplished, deviation is too large". If I reduce the value of tgtmdfrc, there won't be this error but targeted MD will not work, either.
Are there probably some deeper problems with the minimization or heating process of the system? Or I just need to adjust the atommask and tgtmdfrc value?
Thank you!
Best,
Yao Li
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Received on Sat Jul 28 2018 - 10:00:03 PDT
