AMBER Archive (2002)

Subject: Re: problem with gibbs !!!!

From: James W. Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Tue Oct 22 2002 - 09:34:23 CDT

Your problem is not in your input, you simply ran out of
memory. If buying more memory or moving to a bigger
machine is not an option then you must reduce the cutoff.
The parm94 ff was parameterized based on an 8 ang. cutoff.

jim

On Mon, 21 Oct 2002, Asif Rahaman wrote:

>Dear Amber-Users:
> I am trying to calculate free energy change for moving atom
>#3295 towards atom #2967 keeping the atom #13906 at a fixed position in a
>protein. I use the cutoff = 15. in future I want to use larger cutoff. My
>input file is given below. When I run Gibbs i get the following error. I am
>using AMBER version 5. Can anyone please let me know what changes I need to
>make and compile the code so that I can use larger cutoff ie RESNBA. Please
>be elaborate.
>In addition, if anyone finds anything wrong with my input file please point
>that out.
>Thanking you in advance,
>Asif
>------------------
>error --- last part of the output file.
>------------------
> |
> |
> |
>
> READING MOLECULAR TOPOLOGY FILE (PPARM)
>
> --------------------
> DYNAMIC MEMORY
> ALLOCATED USED
>| INTEGER: 7000000 857097
>| REAL: 7000000 1448407
>| CHARACTER: 291666 87110
>
>| AVAILABLE INTEGER WORDS x 1 N-B PAIRS/WORD = 6142903 MAXIMUM N-B PAIRS
>
> |
> |
> |
>
>-------------------
>Solute/solvent pointers:
> IPTSOL= 913 NATRCM=14208
> IPTRES= 0 IPTATM= 0
> NSPSOL= 0 NSPSTR= 0
> NSOLUT=14208 NATOM =14208
>
>| Total accumulated time: 23.69 (seconds) / 0.01 (hours)
> %GIBBS-I-NEWRUN, Begining NRUN = 1
>
> ERROR from RESNBA: Number of non-bonded pairs exceeds the maximum
> allowable ( 1535725). Increase integer storage.
>
> Shared memory implementation: blew scratch array space in resnba
> for thread 2 with the total pairs exceeding the value reported above.
> The actual total effective number of allowable pairs is 6142900.
>-----------------------------
> Here is my input file:
>---------------------------------
> Title
> &cntrl irest=0, ibelly=1,
> ntx=1, ntxo=1, ig=150899, tempi=300.0,
> ntb=0,
> nrun=51, ntt=1, temp0=300.0, dtemp=00.0, tautp=0.2,
> ndfmin = 0, ntcm = 1, nscm = 0,
> nstlim = 2000, init = 3, t=0.0, dt=0.001,
> ntc=2, tol=0.0005, ncorc=1, itimth = 0, ibigm = 1, ishkfl=1, jfastw = 0,
> ntf=1, ntid=0, ntnb=1, nsnb=1000, idiel=1, intprt=5,
> cut=15.0, cut2nd=0.0, scnb = 2.0, scee = 1.2, dielc = 1.0,
> ntpr=100, ntwx=1000, ntwv=-1, ntwe=10, ioutfm=0, isande=1, iperat=1,
> ntwxm = 999999, ntwvm = 999999, ntwem = 999999,
> ntr=1, ntrx=1, intr=1, iatcmp=1, ntatdp=-1,
> almda = 1.0, almdel = 0.02, isldyn = -3, idifrg = 0,
> nstmeq = 1000, nstmul = 1000, ndmpmc = 1, idwide = 0,
> &end
>set restraints on evaporating waters for glh
>1.50
>RES 867 867 869 869 872 875 881 881 883 884 895 895
>END
>END
>designating the belly for molecular dynamics
>RES 1 6 9 10 22 46 92 104 106 108 111 114 116 127
>RES 170 200 206 247 249 250 284 287
>RES 296
>RES 298 299 312 313 315 328
>RES 408
>RES 411 412 415 416 419 426 428 429
>RES 432
>RES 482 555 588 610
>RES 612
>RES 620 628
>RES 645
>RES 664 666
>RES 685
>RES 692
>RES 694 695
>RES 700
>RES 740 745
>RES 747
>RES 829 830 835 861
>RES 864 864 867 867 871 875 878 879 881 881 884 889
>RES 892 893 895 895 897 898 900 900 904 906 909 909
>RES 913
>END
>END
> 2967 3295 0000 0000 0 0 2 1.00000 0.00000
>0610.00000 999.99900 610.00000 2.00000 0 0
> 2967 13906 0000 0000 0 0 1 1.00000 1.00000
>0610.00000 999.99999 610.00000 999.99999 0 0
> 

-- 

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James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
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