Hi,
Not sure if this will help, but why are you starting your system with
an initial temperature of 10.0 K (irest = 0, ntx = 1, and tempi =
10.0)? I think you may be asking too much from the thermostat to jump
from 10.0 K to 300.0 K in only a few steps. Maybe try just setting
your initial temperature to 300.0 K (tempi = 300.0) and equilibrate
from there. Also, if you're still trying to equilibrate you may want
to use a smaller time step (something like dt = 0.001).
-Dan
On Sat, Jun 22, 2013 at 9:09 AM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Jun 22 2013 - 10:00:02 PDT
