Dear Wook,
could you please send me directly a restart and a prmtop file so I can
try something ?
Thanks !
On 2/14/11 11:06 AM, Wook Lee wrote:
> 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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>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Mon Feb 14 2011 - 11:00:02 PST
