What is happening at atoms 88/89?
* NITER, NIT, LL, I and J are : 0 0 26 88 89*
Maybe you have a corrupted restrt file from the previous run. Can you
generate a pdb from it, and if so, look at those atoms?
Bill
On 7/6/16 11:23 PM, ATUL KUMAR wrote:
> 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
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>>>>
>>> _______________________________________________
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>>
>>
>> --
>> -------------------------
>> 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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>>
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Received on Thu Jul 07 2016 - 02:00:02 PDT
