it might be worth a test run with shorter nstlim and ntpr=1 so you can see
if any output is produced. the equil.out file before looks like no MD gets
done, so it would make sense that you don't get mdcrd output.
you might also try single processor as a test, sometimes if there is an
error in parallel (like a shake failure) it might not get written to the
output file unless it happens on the master process.
On Tue, May 4, 2010 at 10:15 AM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> Dear Amber users, I am trying to run molecular dynamics on cluster and
> experince strange problem which I haven't seen before.
> I am doing the MM PBSA preparation runs according to MM-PBSA tutorial. I
> get the .rst file at equilibrium stage, but nothing is written in .mdrcd
> file and it's empty. I am not sure if the proble is on cluster side or
> Amber, so I've decied to ask it here as well. Below are equil.in and
> equil.out files and density .rst was used as coordinate file.
> In the end of the list is log from cluster, I guess killing is done if
> software runs with errors too, but I don't see ay obvious errors from
> equil.out
>
> Below is equil.in file:
> hFzd8
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=450000,dt=0.002,
> ntc=2,ntf=2,
> cut=10.0, ntb=2, ntp=1, taup=2.0,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
>
> Below is equil.out file:
>
>
>
> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | Run on 05/03/2010 at 11:04:07
> [-O]verwriting output
>
> File Assignments:
> | MDIN: equil.in
> | MDOUT: equil.out
> |INPCRD: density.rst
> | PARM: fzd8_w.prmtop
> |RESTRT: equil.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: equil.mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
> |
>
> Here is the input file:
>
> hFzd8
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=450000,dt=0.002,
> ntc=2,ntf=2,
> cut=10.0, ntb=2, ntp=1, taup=2.0,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 31.310
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/26/10 Time = 16:52:17
> NATOM = 34010 NTYPES = 17 NBONH = 32026 MBONA = 2046
> NTHETH = 4310 MTHETA = 2786 NPHIH = 8286 MPHIA = 6468
> NHPARM = 0 NPARM = 0 NNB = 61642 NRES = 10302
> NBONA = 2046 NTHETA = 2786 NPHIA = 6468 NUMBND = 47
> NUMANG = 99 NPTRA = 51 NATYP = 31 NPHB = 1
> IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 1716836
> | Hollerith 214364
> | Integer 1043867
> | Max Pairs 19589760
> | nblistReal 408120
> | nblist Int 1112024
> | Total 102382 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
>
>
> General flags:
> imin = 0, nmropt = 0
>
> Nature and format of input:
> ntx = 5, irest = 1, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 5000, ntrx = 1, ntwr =
> 500
> iwrap = 0, ntwx = 5000, ntwv = 0, ntwe =
> 0
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 2, ntb = 2, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Molecular dynamics:
> nstlim = 450000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = 20.00000
>
> Langevin dynamics temperature regulation:
> ig = 71277
> temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
>
> Pressure regulation:
> ntp = 1
> pres0 = 1.00000, comp = 44.60000, taup = 2.00000
>
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 76.693 Box Y = 76.693 Box Z = 76.693
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
> Cutoff= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
>
> begin time read from input coords = 100.000 ps
>
> Number of triangulated 3-point waters found: 10050
>
> Sum of charges from parm topology file = -0.00000018
> Forcing neutrality...
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> | # of SOLUTE degrees of freedom (RNDFP): 70004.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 70004. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> 70004.
> | TOTAL # of degrees of freedom (RNDF) = 70004.
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 11999762
> | TOTAL SIZE OF NONBOND LIST = 11999762
>
>
>
> Cluster LOG:
> Connection to node-15-04 closed by remote host.
> Exit code -5 signaled from node-15-04
> Killing remote processes...Connection to node-18-08 closed by remote host.
> Connection to node-26-01 closed by remote host.
> Connection to node-06-02 closed by remote host.
> Connection to node-50-02 closed by remote host.
> Connection to node-29-04 closed by remote host.
> Connection to node-02-06 closed by remote host.
> Connection to node-01-07 closed by remote host.
> Connection to node-12-04 closed by remote host.
> Connection to node-49-06 closed by remote host.
> Connection to node-03-02 closed by remote host.
> Connection to node-22-01 closed by remote host.
> Connection to node-04-05 closed by remote host.
> Connection to node-55-08 closed by remote host.
> Connection to node-01-03 closed by remote host.
> Connection to node-47-07 closed by remote host.
> DONE
>
>
>
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>
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Received on Tue May 04 2010 - 08:00:05 PDT
