That's the plan - hopefully we can have a bugfix out soon.
All the best
Ross
On 10/26/14, 2:15 PM, "Gonzalo Jimenez" <gonzalojimenezoses.gmail.com>
wrote:
>Hi Ross,
>
>Thanks, it works exactly as you said: by using ntpr <= 999, the
>temperature
>is maintained nicely at 300 K. The performance is degraded a little bit
>due
>to more intensive I/O, and the output files are larger, but the results
>are
>good.
>Maybe you guys can patch it in one of next bugfixes.
>Thanks a lot for your help,
>Best regards,
>Gonzalo
>
>
>-----Mensaje original-----
>From: Ross Walker
>Sent: Sunday, October 26, 2014 1:22 PM
>To: AMBER Mailing List
>Subject: Re: [AMBER] Temperature not correctly maintained using AMBER14
>
>Hi Gonzalo,
>
>I managed to reproduce this. Strangely it seems to only be a problem if
>ntpr>=vrand (the combination of which is not in the test suite). So please
>try setting ntpr = 500 for your system and see if it then appears to work.
>I will setup a bug report to track this.
>
>All the best
>Ross
>
>
>
>On 10/25/14, 7:41 PM, "Gonzalo Jimenez" <gonzalojimenezoses.gmail.com>
>wrote:
>
>>Hi Ross,
>>
>>Thanks for your quick response and sorry for not specifying the
>>executable I was using. I am running the simulation with pmemd.cuda. For
>>your consideration, I pasted the initial part of the output file at the
>>end of this email.
>>
>>The Run.vrand test using pmemd.cuda seems to be passed, although with
>>numerical differences (output attached).
>>
>>This problem seems to happen only with pmemd.cuda. With pmemd the
>>temperature is kept constant at 300 K, as happened in pmemd.cuda in
>>AMBER12.
>>
>>Just changing ntt=2 to ntt=3 keeps the temperature constant at 300 K, so
>>I guess only Andersen thermostat (which is faster than Langevin in our
>>hands) is failing here.
>>I wonder if other users experienced the same issues.
>>
>>Thanks a lot,
>>Gonzalo
>>
>>*************************************************************************
>>*
>>*********************************************************************
>>
>> -------------------------------------------------------
>> Amber 14 SANDER 2014
>> -------------------------------------------------------
>>
>>| PMEMD implementation of SANDER, Release 14
>>
>>| Run on 10/23/2014 at 04:42:19
>>
>>| Executable path: /usr/local/amber14/amber14//bin/pmemd.cuda
>>| Working directory: /nfs/home/gonzalo/sim56
>>| Hostname: seaquest2
>>
>> [-O]verwriting output
>>
>>File Assignments:
>>| MDIN: md2.in
>>
>>| MDOUT: md2.out
>>
>>| INPCRD: md.rst
>>
>>| PARM: sim56.prmtop
>>| RESTRT: md2.rst
>>
>>| REFC: md.rst
>>
>>| MDVEL: mdvel
>>
>>| MDEN: mden
>>
>>| MDCRD: mdcrd_MD2
>>
>>| MDINFO: mdinfo
>>
>>| MDFRC: mdfrc
>>
>>
>>
>>Here is the input file:
>>
>>production
>>
>>&cntrl
>>
>> imin = 0,
>>
>> irest = 1,
>>
>> ntx = 7,
>>
>> ntb = 1,
>>
>> cut = 8.0,
>>
>> ntr = 0,
>>
>> ntc = 2,
>>
>> ntf = 2,
>>
>> tempi = 300.0,
>>
>> temp0 = 300.0,
>>
>> ntt = 2,
>>
>> ioutfm = 1,
>>
>> iwrap = 1,
>>
>> nstlim = 150000000, dt = 0.002,
>>
>> ntpr = 10000, ntwx = 10000, ntwr = -10000,
>>
>>/
>>
>>
>>
>>
>>|--------------------- INFORMATION ----------------------
>>| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>>| Version 14.0
>>|
>>| 01/31/2014
>>|
>>| Implementation by:
>>| Ross C. Walker (SDSC)
>>| Scott Le Grand (nVIDIA)
>>|
>>| CAUTION: The CUDA code is currently experimental.
>>| You use it at your own risk. Be sure to
>>| check ALL results carefully.
>>|
>>| Precision model in use:
>>| [SPFP] - Mixed Single/Double/Fixed Point Precision.
>>| (Default)
>>|
>>|--------------------------------------------------------
>>
>>|----------------- CITATION INFORMATION -----------------
>>|
>>| When publishing work that utilized the CUDA version
>>| of AMBER, please cite the following in addition to
>>| the regular AMBER citations:
>>|
>>| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
>>| Poole; Scott Le Grand; Ross C. Walker "Routine
>>| microsecond molecular dynamics simulations with
>>| AMBER - Part II: Particle Mesh Ewald", J. Chem.
>>| Theory Comput., 2013, 9 (9), pp3878-3888,
>>| DOI: 10.1021/ct400314y.
>>|
>>| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
>>| Duncan Poole; Scott Le Grand; Ross C. Walker
>>| "Routine microsecond molecular dynamics simulations
>>| with AMBER - Part I: Generalized Born", J. Chem.
>>| Theory Comput., 2012, 8 (5), pp1542-1555.
>>|
>>| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
>>| "SPFP: Speed without compromise - a mixed precision
>>| model for GPU accelerated molecular dynamics
>>| simulations.", Comp. Phys. Comm., 2013, 184
>>| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
>>|
>>|--------------------------------------------------------
>>
>>|------------------- GPU DEVICE INFO --------------------
>>|
>>| CUDA_VISIBLE_DEVICES: not set
>>| CUDA Capable Devices Detected: 2
>>| CUDA Device ID in use: 1
>>| CUDA Device Name: GeForce GTX 780
>>| CUDA Device Global Mem Size: 3071 MB
>>| CUDA Device Num Multiprocessors: 12
>>| CUDA Device Core Freq: 0.90 GHz
>>|
>>|--------------------------------------------------------
>>
>>
>>| Conditional Compilation Defines Used:
>>| PUBFFT
>>| BINTRAJ
>>| CUDA
>>| EMIL
>>
>>| Largest sphere to fit in unit cell has radius = 34.952
>>
>>| New format PARM file being parsed.
>>| Version = 1.000 Date = 10/15/14 Time = 13:47:27
>>
>>| 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
>>
>>-------------------------------------------------------------------------
>>-
>>------
>> 1. RESOURCE USE:
>>-------------------------------------------------------------------------
>>-
>>------
>>
>>getting new box info from bottom of inpcrd
>>NATOM = 48510 NTYPES = 19 NBONH = 44770 MBONA = 3818
>>NTHETH = 8484 MTHETA = 5174 NPHIH = 16487 MPHIA = 13426
>>NHPARM = 0 NPARM = 0 NNB = 95981 NRES = 14157
>>NBONA = 3818 NTHETA = 5174 NPHIA = 13426 NUMBND = 82
>>NUMANG = 172 NPTRA = 77 NATYP = 50 NPHB = 1
>>IFBOX = 2 NMXRS = 85 IFCAP = 0 NEXTRA = 0
>>NCOPY = 0
>>
>>| Coordinate Index Table dimensions: 16 16 16
>>| Direct force subcell size = 5.3509 5.3509 5.3509
>>
>> BOX TYPE: TRUNCATED OCTAHEDRON
>>
>>-------------------------------------------------------------------------
>>-
>>------
>> 2. CONTROL DATA FOR THE RUN
>>-------------------------------------------------------------------------
>>-
>>------
>>
>>default_name
>>
>>
>>General flags:
>> imin = 0, nmropt = 0
>>
>>Nature and format of input:
>> ntx = 7, irest = 1, ntrx = 1
>>
>>Nature and format of output:
>> ntxo = 1, ntpr = 10000, ntrx = 1, ntwr =
>>-10000
>> iwrap = 1, ntwx = 10000, ntwv = 0, ntwe =
>> 0
>> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
>> 0
>>
>>Potential function:
>> ntf = 2, ntb = 1, 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 = 0
>>
>>Molecular dynamics:
>> nstlim = 150000000, nscm = 1000, nrespa = 1
>> t = 0.00000, dt = 0.00200, vlimit = -1.00000
>>
>>Anderson (strong collision) temperature regulation:
>> ig = 71277, vrand = 1000
>> temp0 = 300.00000, tempi = 300.00000
>>
>>SHAKE:
>> ntc = 2, jfastw = 0
>> tol = 0.00001
>>
>>| Intermolecular bonds treatment:
>>| no_intermolecular_bonds = 1
>>
>>| Energy averages sample interval:
>>| ene_avg_sampling = 10000
>>
>>Ewald parameters:
>> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
>> 1
>> vdwmeth = 1, eedmeth = 1, netfrc = 1
>> Box X = 85.615 Box Y = 85.615 Box Z = 85.615
>> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
>> NFFT1 = 96 NFFT2 = 96 NFFT3 = 96
>> Cutoff= 8.000 Tol =0.100E-04
>> Ewald Coefficient = 0.34864
>> Interpolation order = 4
>>
>>-------------------------------------------------------------------------
>>-
>>------
>> 3. ATOMIC COORDINATES AND VELOCITIES
>>-------------------------------------------------------------------------
>>-
>>------
>>
>>default_name
>>
>>begin time read from input coords =202100.000 ps
>>
>>
>>Number of triangulated 3-point waters found: 13687
>>
>> Sum of charges from parm topology file = -0.00000621
>> Forcing neutrality...
>>
>>| Dynamic Memory, Types Used:
>>| Reals 1341211
>>| Integers 1839531
>>
>>| Nonbonded Pairs Initial Allocation: 8102382
>>
>>| GPU memory information (estimate):
>>| KB of GPU memory in use: 294369
>>| KB of CPU memory in use: 62817
>>
>>-------------------------------------------------------------------------
>>-
>>------
>> 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
>>|---------------------------------------------------
>>Setting new random velocities at step 1000
>>check COM velocity, temp: 0.001271 0.00(Removed)
>>Setting new random velocities at step 2000
>>check COM velocity, temp: 0.002907 0.01(Removed)
>>Setting new random velocities at step 3000
>>check COM velocity, temp: 0.001948 0.01(Removed)
>>Setting new random velocities at step 4000
>>check COM velocity, temp: 0.001399 0.00(Removed)
>>Setting new random velocities at step 5000
>>check COM velocity, temp: 0.003220 0.02(Removed)
>>Setting new random velocities at step 6000
>>check COM velocity, temp: 0.003343 0.02(Removed)
>>Setting new random velocities at step 7000
>>check COM velocity, temp: 0.003447 0.02(Removed)
>>Setting new random velocities at step 8000
>>check COM velocity, temp: 0.001476 0.00(Removed)
>>Setting new random velocities at step 9000
>>check COM velocity, temp: 0.000991 0.00(Removed)
>>Setting new random velocities at step 10000
>>check COM velocity, temp: 0.001625 0.00(Removed)
>>wrapping first mol.: -57.07654 40.35921 69.90421
>>writing md2.rst_10000
>>
>>
>>
>>wrapping first mol.: -57.07654 40.35921 69.90421
>>
>>NSTEP = 10000 TIME(PS) = 202120.000 TEMP(K) = 0.91 PRESS =
>> 0.0
>>Etot = -145953.8202 EKtot = 91.3135 EPtot =
>>-146045.1337
>>BOND = 1381.5973 ANGLE = 3836.8153 DIHED =
>>5299.1263
>>1-4 NB = 1694.1473 1-4 EEL = 19271.0073 VDWAALS =
>>15393.3846
>>EELEC = -192921.2118 EHBOND = 0.0000 RESTRAINT =
>>0.0000
>>-------------------------------------------------------------------------
>>-
>>----
>>
>>Setting new random velocities at step 11000
>>check COM velocity, temp: 0.001552 0.00(Removed)
>>Setting new random velocities at step 12000
>>check COM velocity, temp: 0.001903 0.01(Removed)
>>Setting new random velocities at step 13000
>>check COM velocity, temp: 0.002350 0.01(Removed)
>>Setting new random velocities at step 14000
>>check COM velocity, temp: 0.002269 0.01(Removed)
>>Setting new random velocities at step 15000
>>check COM velocity, temp: 0.000604 0.00(Removed)
>>Setting new random velocities at step 16000
>>check COM velocity, temp: 0.002395 0.01(Removed)
>>Setting new random velocities at step 17000
>>check COM velocity, temp: 0.002963 0.01(Removed)
>>Setting new random velocities at step 18000
>>check COM velocity, temp: 0.003513 0.02(Removed)
>>Setting new random velocities at step 19000
>>check COM velocity, temp: 0.002791 0.01(Removed)
>>Setting new random velocities at step 20000
>>check COM velocity, temp: 0.002330 0.01(Removed)
>>wrapping first mol.: -57.07654 40.35921 69.90421
>>writing md2.rst_20000
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>-----Mensaje original-----
>>From: Ross Walker
>>Sent: Saturday, October 25, 2014 6:44 PM
>>To: AMBER Mailing List
>>Subject: Re: [AMBER] Temperature not correctly maintained using AMBER14
>>
>>Hi Gonzalo,
>>
>>Is this sander, sander.MPI, pmemd, pmemd.MPI, pmemd.cuda or
>>pmemd.cuda.MPI?
>>
>>Do the test cases pass - in particular Run.vrand in 4096wat and
>>cuda/4096wat?
>>
>>And is there a difference if you use sander vs pmemd vs pmemd.cuda?
>>
>>All the best
>>Ross
>>
>>
>>On 10/25/14, 6:07 PM, "Gonzalo Jimenez" <gonzalojimenezoses.gmail.com>
>>wrote:
>>
>>>Hi,
>>>
>>>I am experiencing weird issues with temperature control in AMBER14. This
>>>is my input file:
>>>
>>>production
>>>&cntrl
>>> imin = 0,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 1,
>>> cut = 8.0,
>>> ntr = 0,
>>> ntc = 2,
>>> ntf = 2,
>>> tempi = 300.0,
>>> temp0 = 300.0,
>>> ntt = 2,
>>> ioutfm = 1,
>>> iwrap = 1,
>>> nstlim = 500000000, dt = 0.002,
>>> ntpr = 10000, ntwx = 10000, ntwr = -10000,
>>>/
>>>
>>>
>>>
>>>It works nicely in AMBER12, and keeps temperature at 300+-2 K, but in
>>>AMBER14, the temperature is constant, but 40K above!:
>>>
>>>md8.out: NSTEP = 33630000 TIME(PS) = 2069360.003 TEMP(K) = 339.36
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33640000 TIME(PS) = 2069380.003 TEMP(K) = 341.18
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33650000 TIME(PS) = 2069400.003 TEMP(K) = 340.15
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33660000 TIME(PS) = 2069420.003 TEMP(K) = 340.09
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33670000 TIME(PS) = 2069440.003 TEMP(K) = 339.43
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33680000 TIME(PS) = 2069460.003 TEMP(K) = 339.60
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33690000 TIME(PS) = 2069480.003 TEMP(K) = 339.53
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33700000 TIME(PS) = 2069500.003 TEMP(K) = 339.43
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33710000 TIME(PS) = 2069520.003 TEMP(K) = 339.41
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33720000 TIME(PS) = 2069540.003 TEMP(K) = 339.10
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33730000 TIME(PS) = 2069560.003 TEMP(K) = 342.46
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33740000 TIME(PS) = 2069580.003 TEMP(K) = 339.59
>>>PRESS = 0.0
>>>md8.out: NSTEP = 33750000 TIME(PS) = 2069600.003 TEMP(K) = 339.71
>>>PRESS = 0.0
>>>
>>>
>>>Why is that? Is it a bug or just a printing problem?
>>>
>>>Thanks a lot,
>>>Gonzalo
>>>_______________________________________________
>>>AMBER mailing list
>>>AMBER.ambermd.org
>>>http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>_______________________________________________
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>>_
>>____________________
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>>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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>
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Received on Sun Oct 26 2014 - 19:00:01 PDT
