1. Yes I equilibrated the complex in water for 40ns before adding ethanols.
2, Input file for heating. I don't have a large cutoff.
tlr3 protein dimer rna and glycam in tip3p water/EtOH
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 8.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 10.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 25000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000
/
keep the protein fixed with weak retraints
10.0
RES 1 1512
END
END
3. It prints few steps before fails.
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 14.61 PRESS
= 0.0
Etot = -1095540.5600 EKtot = 7734.6283 EPtot =
-1103275.1883
BOND = 1876.5491 ANGLE = 4746.2093 DIHED =
23611.6290
1-4 NB = 5225.3840 1-4 EEL = 48461.7044 VDWAALS =
173588.8603
EELEC = -1360785.5244 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2014E-03
------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 201.87 PRESS =
0.0
Etot = -768689.8911 EKtot = 106903.0375 EPtot =
-875592.9286
BOND = 4463.9266 ANGLE = 10321.5612 DIHED =
24696.2491
1-4 NB = 5579.7819 1-4 EEL = 48351.5207 VDWAALS =
132666.3181
EELEC = -1104811.7543 EHBOND = 0.0000 RESTRAINT =
3139.4680
EAMBER (non-restraint) = -878732.3967
Ewald error estimate: 0.8889E-04
4. If works with serial runs.. So do I have to do this for ever. This will
take huge amount of time.
Thank you
Chinthaka
On Sat, Jun 22, 2013 at 7:48 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Sat, Jun 22, 2013, Chinthaka Ratnaweera wrote:
>
> > Complete error msg as follows
> > ***** System must be very inhomogeneous.
> > ***** Readjusting recip sizes.
> > In this slab, Atoms found: 119297 Allocated: 91707
> >
> >
> > * NB pairs 216 21628899 exceeds capacity ( 21629083) 3
> > SIZE OF NONBOND LIST = 21629083
> > SANDER BOMB in subroutine nonbond_list
> > Non bond list overflow!
> > check MAXPR in locmem.f
>
> Lots of debugging type questions:
>
> 1. Did you equilibrate the system in pure water (with NPT to a good final
> density) before adding a small amount of ethanol? That might help see if
> the
> problem is with the initial packmol setup.
>
> 2. Can you post your input file? It looks like you might have a large
> value
> of cut(?).
>
> 3. Do short simulations and print often. Does the error happen right at
> the
> beginning? Look carefuly at the density vs. time: is the system volume
> changing quickly?
>
> 4. Try some runs with the serial version of the code (it doesn't care about
> how atoms are allocated among processors.) Again, these should be short
> runs,
> printing out often, so you can try to figure out what is happening.
>
> ...dac
>
>
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>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Sat Jun 22 2013 - 08:30:03 PDT
