[AMBER] Several questions about Amber adaptive QM/MM MD.

From: Mingyuan_xu <ming_yxu.163.com>
Date: Tue, 19 Dec 2017 00:39:00 +0800 (CST)

Dear Amber members:
I have meet several questions about Amber adaptive QM/MM MD. I am doing a QM/MM umbrella sampling to scan the potential energy surface and the QM theory for A region is DFTB3. I found out that several water molecules fluctuate very fast and the DFTB3 calculations could not achieve convergent result after 50 time steps,then the sander bombed¡£Before each QM/MM calculations, I have run several picoseconds MM MD to make sure the structure normal. My input file md_equil.in is shown as follows:

50 ps equilibration for Zn and COO
  imin = 0, ntx = 1, irest = 0,
  ntpr = 1, ntwr = 1, ntwx = 1,
  ntf = 1, ntc = 1, cut = 999.0,
  ntb = 0, nstlim = 10000, dt = 0.001,
  tempi=300.0, temp0 = 300.0, ntt = 6,
  gamma_ln = 1.0,igb=0,
  nmropt = 1, ioutfm=0,
  ntr=1,restraintmask='.5 ',restraint_wt=300.0,
    qmmask=':1,2',# the Zinc ion and a COO-
    qm_center_atom_id=5 # atom index of CD atom in COO-
    n_partition =10

     And my prmtop file and initial coordinate file are listed in accessory. To solve this problem, I have test different values of n_partition parameter, but the results are almost the same¡£
     Could you help me? It's really my honor to receive any letter from you£¬thank you ¡£
                             Best wishes for you!

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Received on Mon Dec 18 2017 - 09:00:02 PST
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