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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Received on Sun Oct 26 2014 - 14:30:02 PDT
