what do the temperatures etc look like up
until it stops? is it stable, or did the T go up?
Carlos
----- Original Message -----
From: "Shuang Ding" <sd517.nyu.edu>
To: <amber.heimdal.compchem.ucsf.edu>
Sent: Thursday, May 29, 2003 4:47 PM
Subject: MD problem
> 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.
>
>
>
Received on Thu May 29 2003 - 21:53:02 PDT
