tang kwa wrote:
>
> Dear all,
>
> Following the tutorial in AMBER website,in the MD
> simulation using belly (at 940th step), the simulation
> was stoped with error message
>
> EWALD BOMB in subroutine ewald_list
> volume of ucell too big, too many subcells
> list grid memory needs to be reallocated, restart
> sander
It seems the error occurs because the temperature is raised from 100 to
300K using NPT simulation (instead of NVT simulation, which is the
recommended way in general; see p.89 of the manual).
As a workaround: split the calculation into two.
1. Adjust the temp. using NVT simulation, i.e. set ntb=1 in the file
below.
2. Adjust the density using NPT simulation for the system with T~300K,
i.e. set ntb=2 again, tempi=300, nmropt=0, and remove the lines
&wt
type='TEMP0', istep1=0, istep2=1000,
value1=100.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=1000, istep2=12500,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
&end
Best regards
Holger
>
> (see input below, I am using AMBER7 on linux machine)
>
> Could you give me some advices how to solve this
> problem?
> Thanks a lot
> TK
>
> # MD with heating to 500K and then cooling down back
> to
> 300K
> &cntrl
>
> This is input file:
>
> initial dynamics w/ belly on DNA, model1, 9.0 cut
> &cntrl
>
> ntx = 1, irest = 0, ntrx = 1,
> ntxo = 1,
> ntpr = 10, ntwx = 500, ntwv = 0,
> ntwe = 0,
>
> ntf = 2, ntb = 2,
> cut = 9.0, nsnb = 10,
>
> ibelly = 1, ntr = 0,
>
> nstlim = 12500,
> nscm = 0,
> t = 0.0, dt = 0.002,
>
> temp0 = 300.0, tempi = 100.0,
> ig = 71277, heat = 0.0,
> ntt = 1,
> tautp = 0.5,
> vlimit = 20.0,
>
> ntp = 1, pres0 = 1.0, comp = 44.6,
> taup = 0.5, npscal = 1,
>
> ntc = 2, tol = 0.000001,
>
> nmropt = 1,
>
> &end
> &wt
> type='TEMP0', istep1=0, istep2=1000,
> value1=100.0, value2=300.0,
> &end
> &wt
> type='TEMP0', istep1=1000, istep2=12500,
> value1=300.0, value2=300.0,
> &end
> &wt
> type='END',
> &end
> &rst
> iat=0,
> &end
> Allowing only the water and counterions to move in the
> belly
> RES 16 2909
> END
> END
>
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--
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037 USA
phone: +1-858-784-9788
fax: +1-858-784-8896
email: gohlke.scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++
Received on Mon May 26 2003 - 21:53:01 PDT
