AMBER Archive (2002)

Subject: Re: About the sander_classic calculation

From: John Bushnell (bushnell_at_chem.ucsb.edu)
Date: Thu Apr 04 2002 - 16:31:11 CST

Hi,

According to the comment at the top of the file avfrc.h
in $AMBERHOME/src/sander_classic MXAAVF is the maximum
number of atoms that can be used with averaged forces.
You probably just need to change this from the default
(which is 25000) to something larger than your system
(26357) in the file avfrc.h. Then recompile sander_classic.
Look at the file 0README in $AMBERHOME/src
for hints. You might have to do a "make clean" first
in $AMBERHOME/src/sander_classic.

     Hope that helps - John

On Thu, 4 Apr 2002, Alan Leo wrote:

> Hi, everyone:
>
> I am using sander_classic in AMBER6 to do MD, It doesnot work at all.
> The output file error message is listed as following:
>
> *******
> | Memory Use Allocated Used
> | Real 3700000 948908
> | Hollerith 600000 219175
> | Integer 2000000 611602 (static)
>
> | Max Nonbonded Pairs: 9000000 packed 2 to a machine word
> ERROR: MXAAVF in avfrc.h is smaller than the 26357 atoms in this molecule.
> *******
>
> My input file is shown as following to do 600ps MD:
>
> *******
> &cntrl
> timlim = 999999., nmrmax = 0,
> ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 50, ntwr = 0, ntwx = 500, ntwv = 0,
> ntwe = 50, ntwxm = 999999, ntwvm = 999999, ntwem = 999999,
> ioutfm = 0, ntwprt = 0,
>
> ntf = 2, ntb = 2, idiel = 1, dielc = 1.0,
> cut = 9.0, ntnb = 1, nsnb = 25, ntid = 0,
> scnb = 2.0, scee = 1.2, cut2nd = 0.0,
>
> isftrp = 0, rwell = 0.0,
>
> ipol = 0,
>
> ibelly = 0, ntr = 0,
>
> imin = 0,
>
> nrun = 4, nstlim = 100000, ndfmin = 6, ntcm = 1,
> nscm = 0, init = 4, t = 0.0, dt = 0.0015,
>
> temp0 = 400.0, tempi = 400.0, ig = 71477, heat = 0.0,
> ntt = 5, isolvp = 0, dtemp = 0.0,
> tautp = 0.1, tauts = 0.1, vlimit = 20.0,
>
> tauv0 = 0.0, tauv = 0.1, vzero = 0.0,
>
> ntp = 1, pres0 = 1.0, comp = 44.6,
> taup = 0.2, npscal = 0,
>
> ntc = 2, tol = 1.d-4 ,
>
> imgslt = 0, iftres = 1, jfastw = 0,
>
> &end
> ********
>
> Who can tell me what is the matter with my calculation?
>
> Many thanks in advance!
>
> Sincerely yours
> Alan
>
>