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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Received on Tue May 04 2010 - 07:30:04 PDT
