After running it on CPU version I am getting the following output file
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| Run on 07/07/2016 at 11:48:56
| Executable path: sander
| Working directory:
/home/atul/ATUL_MD/EDO_CRO/Smuln/WATER/Restrain_Trjectory_for_GIST
| Hostname: pblab1
[-O]verwriting output
File Assignments:
| MDIN: restart.in
| MDOUT: test10ns.out
|INPCRD: wat_restrain30ns.rst
| PARM: DNA_Water.prmtop
|RESTRT: test10ns.rst
| REFC: equi5.rst
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: test10ns.nc
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
Here is the input file:
Constant pressure constant temperature production run
&cntrl
nstlim=5000000, dt=0.002, ntx=5, irest=1, ntpr=1500, ntwr=1500,
ntwx=1500,ntr=1,
temp0=300.0, ntt=3, gamma_ln=1.0,
ioutfm = 1, iwrap = 1,
ntb=2, ntp=1,
ntc=2, ntf=2,
&end
Group input for restrained atoms
20.0
RES 1 46
END
END
--------------------------------------------------------------------------------
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 = 48.405
| New format PARM file being parsed.
| Version = 1.000 Date = 11/05/15 Time = 13:09:49
NATOM = 107868 NTYPES = 19 NBONH = 106661 MBONA = 1050
NTHETH = 1224 MTHETA = 1617 NPHIH = 2472 MPHIA = 2936
NHPARM = 0 NPARM = 0 NNB = 149889 NRES = 35697
NBONA = 1050 NTHETA = 1617 NPHIA = 2936 NUMBND = 43
NUMANG = 86 NPTRA = 48 NATYP = 30 NPHB = 1
IFBOX = 1 NMXRS = 33 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 7638826
| Hollerith 359303
| Integer 2733553
| Max Pairs 35956000
| nblistReal 1294416
| nblist Int 5047297
| Total 242041 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
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 = 1500, ntrx = 1, ntwr =
1500
iwrap = 1, ntwx = 1500, ntwv = 0, ntwe =
0
ioutfm = 1, 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 = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 0.00000
Molecular dynamics:
nstlim = 5000000, nscm = 0, 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= 1.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
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 = 96.809 Box Y = 96.809 Box Z = 116.171
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 96 NFFT2 = 96 NFFT3 = 120
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
----- READING GROUP 1; TITLE:
Group input for restrained atoms
GROUP 1 HAS HARMONIC CONSTRAINTS 20.00000
GRP 1 RES 1 TO 46
Number of atoms in this group = 1455
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 30069.000 ps
Number of triangulated 3-point waters found: 35381
Sum of charges from parm topology file = 0.00000027
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 216943.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 216943. NUM_NOSHAKE = 0 CORRECTED RNDFP = 216943.
| TOTAL # of degrees of freedom (RNDF) = 216943.
---------------------------------------------------
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 = 0.8332E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 22228269
| TOTAL SIZE OF NONBOND LIST = 22228269
*vlimit exceeded for step 0; vmax = 190.1244*
*vlimit exceeded for step 1; vmax = 208.2801*
*vlimit exceeded for step 2; vmax = ***********
* Coordinate resetting (SHAKE) cannot be accomplished,*
* deviation is too large*
* NITER, NIT, LL, I and J are : 0 0 26 88 89*
* Note: This is usually a symptom of some deeper*
* problem with the energetics of the system.*
*Atul Kuamr jaiswal*
Research Scholar
School of Computational and Integrative Sciences
Centre for Computational Biology and Bioinformatics (CCBB)
JNU,New Delhi
India.
On Wed, Jul 6, 2016 at 9:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Wed, Jul 6, 2016 at 7:43 AM, ATUL KUMAR <atul44_sit.jnu.ac.in> wrote:
> > Thank you for the reply I forgot to mention the directed error file. The
> > error printed in the error file is here:
> >
> > *cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> > encountered*
>
> Can you try restarting the calculation using CPU code? If there are
> any energetic/force issues causing the simulation to crash the CPU
> code may provide a more informative message.
>
> -Dan
>
> >
> > *Atul Kuamr jaiswal*
> > Research Scholar
> > School of Computational and Integrative Sciences
> > Centre for Computational Biology and Bioinformatics (CCBB)
> > JNU,New Delhi
> > India.
> >
> > On Wed, Jul 6, 2016 at 6:23 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> >> On Wed, Jul 6, 2016 at 7:38 AM, ATUL KUMAR <atul44_sit.jnu.ac.in>
> wrote:
> >>
> >> > Dear Amber users,
> >> > I have run a simulation of 30ns with the input file give below
> >> >
> >> > *Constant pressure constant temperature production run*
> >> > * &cntrl*
> >> > * nstlim=15000000, dt=0.002, ntx=5, irest=1, ntpr=1500, ntwr=1500,
> >> > ntwx=1500,ntr=1,*
> >> >
> >> > * temp0=300.0, ntt=3, gamma_ln=1.0,*
> >> >
> >> > * ioutfm = 1, iwrap = 1,*
> >> >
> >> > * ntb=2, ntp=1,*
> >> >
> >> > * ntc=2, ntf=2,*
> >> > *&end*
> >> > *Group input for restrained atoms*
> >> > *20.0*
> >> > *RES 1 46*
> >> > *END*
> >> > *END*
> >> >
> >> > When I am trying to extend the simulation after 30 nano second I am
> >> getting
> >> > following error in the end of .out file
> >> >
> >> >
> >> >
> >> >
> >>
> *--------------------------------------------------------------------------------*
> >> > * 4. RESULTS*
> >> >
> >> >
> >>
> *--------------------------------------------------------------------------------*
> >> >
> >> > * ---------------------------------------------------*
> >> > * 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 = 0.8332E-11 at 2.782960*
> >> > * ---------------------------------------------------*
> >> > *|---------------------------------------------------*
> >> > *| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION*
> >> > *| with 50.0 points per unit in tabled values*
> >> > *| Relative Error Limit not exceeded for r .gt. 2.47*
> >> > *| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION*
> >> > *| with 50.0 points per unit in tabled values*
> >> > *| Relative Error Limit not exceeded for r .gt. 2.89*
> >> > *|---------------------------------------------------*
> >> >
> >>
> >> There is no error here. Was the error maybe printed to the screen or to
> >> the standard error stream (which may have been captured in an "error"
> file
> >> if you submitted to a queue)? There's not even enough information here
> to
> >> tell us a problem occurred, let alone how to fix it.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Wed Jul 06 2016 - 23:30:02 PDT
