AMBER Archive (2007)

Subject: Re: AMBER: error when using sander.LES: exceeded MAXLES

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jan 18 2007 - 11:03:08 CST

you need to change MAXLES for sander, which is in sander/les.h
1000 copies is very high, make sure you know what you're
doing.

Kailee wrote:

> Dear all AMBER users,
>
> I have a problem when I tried to use sander.LES (with amber8). Here
> are the procedures I used it:
>
> First, I minimized my non-LES system, and heated it up from 0K to
> 300K. Then I used 'addles' to prepare the inputs for the LES. When I
> used 'addles', I had the error about exceeding the compilation limit,
> and therefore I modified the SIZE.h file and recompile addles. Then
> everything was OK when I run 'addles' again. And this is the input for
> addles:
> #######################################################
> file rprm name=(LES_ini.prmtop) read
> file rcvb name=(heat.rst) read
> file wprm name=(LES.prmtop) wovr
> file wcrd name=(LES.crd) wovr
> action
> omas
> spac numc=1000 pick #mon 792 792 done
> *EOD
> ######################################################
>
> And I run molecular dynamics using LES, this is the input file (md1.in
> <http://md1.in>):
> ########################################################
> LES_md1
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 100000, dt = 0.001,
> ntpr = 200, ntwx = 200, ntwr = 2000
> /
> ##########################################################
>
> And I run the job using:
> $AMBERHOME/exe/sander.LES -O -i LES_md1.in -o LES_md1.out -p
> LES.prmtop -c LES.crd -r LES_md1.rst -x LES_md1.mdcrd
>
> And here is the output I got:
> ############################################################
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
> | Run on 01/18/2007 at 16:15:37
> [-O]verwriting output
>
> File Assignments:
> | MDIN: LES_md1.in
> | MDOUT: LES_md1.out
> |INPCRD: LES.crd
> | PARM: LES.prmtop
> |RESTRT: LES_md1.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: LES_md1.mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
>
> Here is the input file:
>
> LES_md1
>
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 100000, dt = 0.001,
> ntpr = 200, ntwx = 200, ntwr = 2000
> /
>
>
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags: MPI LES
> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 38.199
> NATOM = 57536 NTYPES = 19 NBONH = 50378 MBONA = 6328
> NTHETH = 13715 MTHETA = 8660 NPHIH = 25765 MPHIA = 16154
> NHPARM = 0 NPARM = 1 NNB = 2124220 NRES = 15260
> NBONA = 6328 NTHETA = 8660 NPHIA = 16154 NUMBND = 68
> NUMANG = 142 NPTRA = 44 NATYP = 44 NPHB = 1
> IFBOX = 1 NMXRS = 2000 IFCAP = 0 NEXTRA = 0
> NCOPY = 1000
>
>
> | Memory Use Allocated
> | Real 4023896
> | Hollerith 360478
> | Integer 23531916
> | Max Pairs 8285184
> | Max Rstack 2199202
> | Max Istack 287680
> | Total 175435 kbytes
> Exceeded MAXLES 57536
> #########################################################################
>
>
>
> Can anyone please tell me what is the problem here? it said " Exceeded
> MAXLES 57536", where 57536 is the total atom number in the LES
> system. Howeverm I have changed 'maxnatom=70000' in the SIZE.h file
> before I recompile addles. Thank you for all your help in advance!
>
> Best regards,
>
> Kailee
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu