AMBER Archive (2003)

Subject: Re: MD problem

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Thu May 29 2003 - 16:14:14 CDT

Can you check what atom 172 and 173 are in your system and what they were
doing in the last saved restart file? I just wonder if they were part of your
"bulky adduct".

On Thursday 29 May 2003 16:47, Shuang Ding wrote:
> Hi,
>
> I'm running an MD simulation of a DNA 11-mer damaged covalently with a
> bulky adduct attached to one base. However the simulation was stopped after
> 50ps of production in AMBER 7 with error message: " vlimit exceeded for
> step 50582; vmax = 26.05232686120750 vlimit exceeded for step
> 50583; vmax = 24.16632764793692 EWALD BOMB in subroutine ewald_list
> volume of ucell too big, too many subcells
> list grid memory needs to be reallocated, restart sander"
>
> Equilibration was performed normally as in the DNA tutorial (minimized for
> 1000 steps of steepest descent, followed by 50ps dynamics with DNA fixed to
> relax the water, then minimized for 1000 additional steps of steepest
> descent, follow by 3ps dynamic with 25kcal/mol restraints on the DNA, five
> rounds minimization of 600 steps with restraint reduced by 5kal/mol each
> round, from 20 to 0kal/mol. Finally heated up from 10k to 300k over 40ps,
> and additional 20ps unrestrained dynamics for equilibration.)
>
> This happens after 58ps of production in AMBER6 too, with error message:
> � vlimit exceeded for step 58303; vmax = 187.5334023293732
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
> NITER, NIT, LL, I AND J ARE : 0 4 63 172 173�
>
> This is my input file for both AMBER 6 and 7:
> &cntrl
> ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
> ntwprt = 0, ntwr = 500,
>
> ntf = 2, ntb = 2, dielc = 1.0,
> cut = 12.0, nsnb = 10,
> scnb = 2.0, scee = 1.2,
>
> ipol = 0,
> ibelly = 0, ntr = 0,
>
> imin = 0,
> nstlim = 200000,
> nscm = 1000,
> t = 0.0, dt = 0.001,
>
> temp0 = 300.0, tempi = 300.0,
> ig = 71277, heat = 0.0,
> ntt = 1, dtemp = 0.0,
> tautp = 1.0,
> vlimit = 20.0,
>
> ntp = 1, pres0 = 1.0, comp = 44.6,
> taup = 1.0, npscal = 1,
>
> ntc = 2, tol = 0.000001,
> &end
>
> Could anyone give some suggestion to solve this problem? Thanks a lot. 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790