what is the value of the RMSD (using that fit mask and rms mask) for your
initial structure?
On Sat, Jul 28, 2018 at 12:59 PM 李耀 <liyao17.mails.tsinghua.edu.cn> wrote:
> 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 - 11:00:02 PDT
