AMBER Archive (2003)

Subject: RE: EWALD BOMB

From: Yong Duan (yduan_at_udel.edu)
Date: Mon May 26 2003 - 18:51:22 CDT

Dear Tang Kwa,

This does not usually happen immediately following the model-building
because there should be sufficient room in the box after that. The
density immediately after model-building (by leap) is typically around
0.8-0.9g/cc.
Let us know if Holger's suggest does not fix the problem and give us a
bit more information.
This problem occurs when the volume expands too much and exceeds the
initial allocation (which allows, I believe, 10-20% expansion in
volume). I would thought your volume should shrink, instead, unless
there are problems elsewhere which overheats the system.

yong

> -----Original Message-----
> From: gohlke_at_scripps.edu [mailto:gohlke_at_scripps.edu]
> Sent: Monday, May 26, 2003 3:58 PM
> To: tang kwa
> Cc: Amber List
> Subject: Re: EWALD BOMB
>
>
> 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
> >
> > __________________________________
> > Do you Yahoo!?
> > The New Yahoo! Search - Faster. Easier. Bingo.
http://search.yahoo.com 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
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_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++