Dear Amber Community,
I am currently trying to do some QM/MM simulations on a drug (DG35; 73
atoms) in a 10A box of methanol using AMBER9. I have minimized the
system, heated it to 300K then equilibrated using PMEMD. Following
this I ran a short QM/MM equilibration before wanting to run a QM/MM
production phase. However, I am unable to do this as I cannot get the
system to equilibrate. Here is my input file for the QM/MM
equilibration:
300K constant temp QMMMMD - 250ps Equilibration
&cntrl
imin=0, irest = 1, ntx = 5,
ntb=2, pres0 = 1.0,
ntp=1, taup=2.0,
ntc=2, ntf=2, cut=6.0,
ntt=1, tempi=300.0, temp0=300.0,
nstlim=250000, dt=0.001,
ntpr=100, ntwx=2500, ifqnt=1
/
&qmmm
qmmask=':1',
qmcharge=0,
qmtheory=1,
qmshake=1,
qm_ewald=1, qm_pme=1
/
I find that I am getting a consistently positive pressure which means
that the volume increases and consequently, the density decreases to
non-natural values for methanol (0.4). It is at this stage that
sander.QMMM crashes due to "volume of ucell too big, too many
subcells".
I have continued the PMEMD simulation into the production phase so I
dont think the problem has to do with the drug-methanol system. I have
also tested the QM/MM equilibration with ntt=3 but got the same
problems.
Can anyone give me any advice on what I should try next or any
literature I should read?
Daniel Oehme
PhD Student
La Trobe University
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Received on Sun Apr 22 2007 - 06:07:38 PDT
