Jason,
The short answer to your question is, yes, without the NEB commands in
the in-file temperature does increase, as expected. Rather than the
in-files, I paste in (below) the top of the "neb.out.000", with and
without NEB commands. These recapitulate the input files, and supply
additional information that may tell you more.
Your observation that breaking down groups in to sub-groups severs the
springs between subgroups is very insightful..Thank you for it.
But it begs further questions! As you know (and is demonstrated below),
sander.MPI insists that np => ng. The Amber14 manual (p. 344) makes the
comment:
"1. The number of CPUs specified must be a multiple of the number of
images. You can run this on a standard desktop computer, but it will
generally be more efficient to run it on a minimum of one processor per
image."
This seems to imply that it is possible to run NEB on a 1-processor (or
small number) machine; it's just not efficient. My conclusion would be
that it is impossible to run a 32 group NEB on a 1 (or 4) processor
machine. Unless I'm missing some other technique for breaking up the
group-number (without breaking the springs between them.)
Bob W,
******************sander.MPI insists np => ng******************************
bobw.winter: ~...A5_nudge_elastic_band/1HEAT [281]> mpirun -np 4
sander.MPI -ng 32 -groupfile groupfile
mpirun -np 4 sander.MPI -ng 32 -groupfile groupfile
Error: specified more groups ( 32 ) than the number of
processors ( 4 ) !
*****************where 1heat.in includes NEB line; temp does not increabo
bw.winter: ~...A5_nudge_elastic_band/1HEAT_setsof4 [289]> more neb.out.000
more neb.out.000
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| Run on 03/22/2015 at 18:41:00
| Executable path: sander.MPI
| Working directory:
/mnt/usb3tb_SD/molmodel_work/Amber/tutorials/A5_nudge_elastic_band/1HEAT
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: ./1heat.in
| MDOUT: ./neb.out.000
|INPCRD: ../str1.inpcrd
| PARM: ../str1.prmtop
|RESTRT: ./neb.r.000
| REFC: refc
| MDVEL: mdvel.000
| MDFRC: mdfrc.000
| MDEN: mden.000
| MDCRD: ./neb.x.000
|MDINFO: ./neb.info.000
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
Alanine NEB initial MD with small K
&cntrl
imin = 0, irest = 0,
ntc=1, ntf=1,
ntpr=500, ntwx=500,
ntb = 0, cut = 999.0, rgbmax=999.0,
igb = 1, saltcon=0.2,
nstlim = 40000, nscm=0,
dt = 0.0005, ig=-1,
ntt = 3, gamma_ln=1000.0,
tempi=0.0, temp0=300.0,
tgtfitmask=":1,2,3",
tgtrmsmask=":1,2,3.N,CA,C",
ineb = 1,skmin = 10,skmax = 10,
nmropt=1,
/
&wt type='TEMP0', istep1=0,istep2=35000,
value1=0.0, value2=300.0
/
&wt type='END'
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 03/22/15 Time = 18:04:23
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 43 MPHIA = 22
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 22 NUMBND = 8
NUMANG = 16 NPTRA = 21 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 4741
| Hollerith 71
| Integer 21091
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 119 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
Note: ig = -1. Setting random seed to 81412 based on wallclock time
in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr
= 500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 1, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.20000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 999.00000 extdiel = 78.50000
alpb = 0
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 40000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00050, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 81412
temp0 = 300.00000, tempi = 0.00000, gamma_ln=1000.00000
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub
= 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| MPI Timing options:
| profile_mpi = 0
The following selection will be used for NEB structure fitting
Mask ":1,2,3" matches 22 atoms
The following selection will be used for NEB force application
Mask ":1,2,3.N,CA,C" matches 5 atoms
Last atom in NEB fitmask or rmsmask is 22
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 35000 0.000000 300.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 22
| Running AMBER/MPI version on 1 nodes
| MULTISANDER: 4 groups. 1 processors out of 4 total.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 66.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 66. NUM_NOSHAKE = 0 CORRECTED RNDFP = 66.
| TOTAL # of degrees of freedom (RNDF) = 66.
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
= 0.0
Etot = -32.7645 EKtot = 0.0000 EPtot = -32.7645
BOND = 0.4957 ANGLE = 1.2919 DIHED = 8.5387
1-4 NB = 3.0084 1-4 EEL = 44.5895 VDWAALS =
-1.8571
EELEC = -70.6175 EGB = -18.2139 RESTRAINT =
0.0000
NEB replicate breakdown:
Energy for replicate 1 = -32.7645
Energy for replicate 2 = -32.7645
Energy for replicate 3 = -32.7645
Energy for replicate 4 = -32.7645
Total Energy of replicates = -131.0582
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 500 TIME(PS) = 0.250 TEMP(K) = 0.00 PRESS
= 0.0
Etot = -32.7645 EKtot = 0.0000 EPtot = -32.7645
BOND = 0.4957 ANGLE = 1.2919 DIHED = 8.5387
1-4 NB = 3.0084 1-4 EEL = 44.5895 VDWAALS =
-1.8571
EELEC = -70.6175 EGB = -18.2139 RESTRAINT =
0.0000
NEB replicate breakdown:
Energy for replicate 1 = -32.7645
Energy for replicate 2 = -32.6046
Energy for replicate 3 = -32.5967
Energy for replicate 4 = -32.7645
Total Energy of replicates = -130.7303
------------------------------------------------------------------------------
****************with NEB commands removed; temp does
increase******************
bobw.winter: ~...A5_nudge_elastic_band/1HEAT [285]> more neb.out.000
more neb.out.000
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| Run on 03/31/2015 at 09:19:40
| Executable path: sander.MPI
| Working directory:
/mnt/usb3tb_SD/molmodel_work/Amber/tutorials/A5_nudge_elastic_band/1HEAT
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: ./1heat.in
| MDOUT: ./neb.out.000
|INPCRD: ../str1.inpcrd
| PARM: ../str1.prmtop
|RESTRT: ./neb.r.000
| REFC: refc
| MDVEL: mdvel.000
| MDFRC: mdfrc.000
| MDEN: mden.000
| MDCRD: ./neb.x.000
|MDINFO: ./neb.info.000
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
Alanine NEB initial MD with small K
&cntrl
imin = 0, irest = 0,
ntc=1, ntf=1,
ntpr=500, ntwx=500,
ntb = 0, cut = 999.0, rgbmax=999.0,
igb = 1, saltcon=0.2,
nstlim = 40000, nscm=0,
dt = 0.0005, ig=-1,
ntt = 3, gamma_ln=1000.0,
tempi=0.0, temp0=300.0,
tgtfitmask=":1,2,3",
tgtrmsmask=":1,2,3.N,CA,C",
nmropt=1,
/
&wt type='TEMP0', istep1=0,istep2=35000,
value1=0.0, value2=300.0
/
&wt type='END'
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 03/22/15 Time = 18:04:23
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 43 MPHIA = 22
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 22 NUMBND = 8
NUMANG = 16 NPTRA = 21 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 4741
| Hollerith 71
| Integer 21091
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 119 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
Note: ig = -1. Setting random seed to 52397 based on wallclock time
in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr
= 500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 1, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.20000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 999.00000 extdiel = 78.50000
alpb = 0
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 40000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00050, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 52397
temp0 = 300.00000, tempi = 0.00000, gamma_ln=1000.00000
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub
= 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| MPI Timing options:
| profile_mpi = 0
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 35000 0.000000 300.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 22
| Running AMBER/MPI version on 1 nodes
| MULTISANDER: 4 groups. 1 processors out of 4 total.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 66.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 66. NUM_NOSHAKE = 0 CORRECTED RNDFP = 66.
| TOTAL # of degrees of freedom (RNDF) = 66.
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
= 0.0
Etot = -32.7645 EKtot = 0.0000 EPtot = -32.7645
BOND = 0.4957 ANGLE = 1.2919 DIHED = 8.5387
1-4 NB = 3.0084 1-4 EEL = 44.5895 VDWAALS =
-1.8571
EELEC = -70.6175 EGB = -18.2139 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 500 TIME(PS) = 0.250 TEMP(K) = 3.96 PRESS
= 0.0
Etot = -32.2488 EKtot = 0.2597 EPtot = -32.5084
BOND = 0.6055 ANGLE = 1.5980 DIHED = 8.5701
1-4 NB = 2.9437 1-4 EEL = 44.3095 VDWAALS =
-1.8693
EELEC = -70.4567 EGB = -18.2092 RESTRAINT =
0.0000
On 3/30/15 6:33 PM, Robert Wohlhueter wrote:
> Working my way through Advanced tutorial A5 (NEB) on a standalone,
> 4-processor, AMD-64 machine, running Amber14, under Ubuntu 14.04.
>
> In section 4, "heating up", I run into the following problem. Though
> everything appears to run alright under sander.MPI, in fact, inspection
> of the "-.out" files, any and all, shows that the temperature is
> remaining at 0 degK. I've checked and rechecked the syntax, especially
> the $wt namespace (&wt type='TEMP0', istep1=0,istep2=35000,value1=0.0,
> value2=300.0). Similar syntax, e.g. in the B0 tutorial ("02_Heat.in"}
> has worked fine..
>
> One additional disclosure, which might be at fault (if it is, then I
> really don't comprehend what's going on in NEB!) Because I have only 4
> processors (so, mpirun -np 4), I can't use "-ng 32", so I have broken up
> the tutorial's "groupfile" into 8 subgroup files, each comprising 4
> lines of the original groupfile. Is that kosher? Is there some reason
> this piecemeal approach might interfere with the replicate communication
> in a way that might prevent temperature ramping?
>
> Any nudges will be appreciated,
>
> Bob Wohlhueter
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 31 2015 - 07:00:04 PDT
