Dear Amber users
I am using Amber 11, and I want to calculate PMF as some bond is broken,
so I did umbrella sampling calculation in combination with QMMMMD with
DFTB, and I got some strange results.
The input scripts are shown below.
&cntrl
imin=0, ntb=0
cut=12.0,
temp0=310.0,
ntt=3, gamma_ln=5.0,
nstlim=100000, dt=0.001,
ntpr=1000, ntwx=1000,ifqnt=1,nmropt=1
/
&qmmm
qmmask='.4504-4514, 4952-4962, 12043-12055',
qmcharge=-1,
qm_theory='DFTB',
qmshake=0,
/
&wt type='DUMPFREQ', istep1=10
/
&wt type='END'
/
DISANG=restraint
DUMPAVE=dist21
restraint file :
&rst iat = 12043, 12044, r1=1.1,r2=2.1,r3=2.1,r4=3.1,rk2=300.00,rk3=300.00
The problem is that the distribution I got from this simulation is too
broad.
It sometimes deviates even 0.5 A at maximum from the reference value.
So I did another simulation with larger biased potential (rk=600), and
it still gave similar huge deviation.
The other strange thing is when I performed the exactly same calculation
in other computer cluster,
It showed a reasonable distribution, so I think this problem may related
to the compliation.
The version of the gcc in the cluster where I got problem is 4.3.3, and
the other is 4.2.2
Both are opteron clusters.
I would really appreciate it if anyone could help me with this problem.
Best regards,
Wook
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Received on Mon Feb 14 2011 - 02:30:02 PST
