AMBER Archive (2003)

Subject: Re: MD problem

From: Shuang Ding (sd517_at_nyu.edu)
Date: Thu May 29 2003 - 16:30:54 CDT

Hi, the atoms 172 and 173 are on the adjacent base next to that adduct.

----- Original Message -----
From: Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
Date: Thursday, May 29, 2003 5:14 pm
Subject: Re: MD problem

> 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
>
>