hi all
I'm doing an one-step TI calculations for a single atom ligand mutation (H
-> F). There are sort of two issues. The first one is as follows:
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1861 Allocated: 1781
This seems like a warning message and does not really stop the simulation.
And I see this from the first step of minimization to the final production
run. I did some research online. It could be a strange starting structure or
density problem. I checked the energy of the first step minimization, it
looks ok. There are no "******" values. One possibility is that I'm using
ntc = 1 with TIP3P water. So I switched to ntf=2, ntc=2. It didn't help.
The other problem is this:
* NB pairs 231 1594826 exceeds capacity ( 1594870) 7
SIZE OF NONBOND LIST = 1594870
SANDER BOMB in subroutine nonbond_list
Non bond list overflow!
check MAXPR in locmem.f
This really pulls the trigger and kills the simulation. I don't know whether
this is an "outcome" of problem 1. Again I searched in AMBER archive and
examined a few things. But nothing seems to be wrong.
Any comment is greatly appreciated.
Btw, I'm pasting the input file for minimization, equilibration and
production run. Hope it helps. (it's a truncated structure so I need apply
some restrains on the outer layers)
minimization
&cntrl
imin = 1, ntx = 1,
maxcyc=1000, ntmin=2,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut =
9.0,
icfe=1, clambda = 0.70, noshakemask=":1",
/
density equilibration
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 2500, ntwr = 10000, ntwx = 0,
ntf = 2, ntc = 2, ntr=1,
ntb = 2, cut = 9.0,
nstlim = 25000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
icfe=1, clambda = 0.70, noshakemask=":1",
/
complex (>8)
8.0
RES 1 3
RES 13 16
RES 19 35
RES 45 56
RES 58 66
RES 73 75
RES 81 87
RES 89 90
END
END
NPT production
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 5000, ntwr = 5000, ntwx = 5000,
ntf = 2, ntc = 2, ntr=1,
ntb = 2, cut = 9.0,
nstlim = 300000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 2,
ntp = 1, pres0 = 1.0, taup = 2.0,
icfe=1, clambda = 0.70, noshakemask=":1",
/
complex (>8)
8.0
RES 1 3
RES 13 16
RES 19 35
RES 45 56
RES 58 66
RES 73 75
RES 81 87
RES 89 90
END
END
Victor
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Received on Tue Sep 20 2011 - 12:30:02 PDT
