VMD-L Mailing List

From: ABEL Stephane 175950 (Stephane.ABEL_at_cea.fr)
Date: Wed Aug 12 2015 - 08:17:26 CDT

Dear all,

I am using fftk (VMD1.92) in a desktop (RAM 4GO , Intel core i5 3371 U @ 1.7Ghz, Graphic card Intel HD 400) with Wndows 7 Pro 64 bits to optimize a molecule with 20 atoms. And unfortunately I have some problems with NAMD during the "Opt Bonded" optimization step used by fftk. The conf and temp OPTTEMP files are well generated and seem correct to me. When I push the "run optimization" button NAMD starts but crashes after few seconds with the following errors :

Charm++: standalone mode (not using charmrun)
Charm++ warning> fences and atomic operations not available in native assembly
Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
[0] isomalloc.c> Disabling isomalloc because mmap() does not work
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).

the tk console doesn't not show (as far I as can tell) useful error message:

------- tk console ----------------------------------

PARAMETERS TO OPTIMIZE
Input Bond Pars:
        {CG321 CG311} 279.9747 1.5413
Input Angle Pars:
----------------------------------

ADVANCED SETTINGS
tol: 0.001
Geom. Weight: 1.0
En. Weight: 1.0
optimization mode: downhill
Downhill settings: Iterations-500
Simulated Annealing settings: Temp-25, Steps-20, Iterations-15
Adv. Bonds: Eq. Dev.-0.25, K LB-0.0 UB-1000.0
Adv. Angles: Eq. Dev.-10.0, K LB-0.0 UB-300.0
debugging: 1
----------------------------------

HARDCODED SETTINGS (set by init)
minName: min-bondangles
tempParName: OPTTEMP.par
bondscale: 0.03
angscale: 3.0
enscale: 1.0
dxBond: 0.1
dxAng: 5.0
----------------------------------
natoms 0; C 0 -3.3223899732 5.757428038 0.7550224557
Cartesian coordinates given.
natoms 1; C 0 -4.3339524412 4.7802126702 0.1245088324
natoms 2; H 0 -3.609055953 5.9629260417 1.7933387172
natoms 3; H 0 -3.3745954707 6.7116099022 0.2216222953
natoms 4; H 0 -4.291104285 3.8264668051 0.6707249661
natoms 5; H 0 -4.0174554463 4.5702383127 -0.9044014531
natoms 6; C 0 -5.7464692289 5.3086932151 0.1283182005
natoms 7; C 0 -6.3725572934 5.4763004251 1.4886826036
natoms 8; H 0 -5.9534958995 6.3386637662 2.019325736
natoms 9; H 0 -6.1740298272 4.5926304372 2.1058331536
natoms 10; H 0 -7.4543330787 5.6116491032 1.4395426118
natoms 11; C 0 -6.3484629405 5.6229532319 -1.0352283244
natoms 12; C 0 -7.7209474035 6.1904701534 -1.2441590676
natoms 13; H 0 -5.7809213918 5.4503625777 -1.9511081231
natoms 14; H 0 -7.6629950471 7.152729398 -1.7653826389
natoms 15; H 0 -8.2584703663 6.3532836597 -0.308672171
natoms 16; H 0 -8.3255639042 5.5256603034 -1.8712887675
natoms 17; C 0 -1.9312789711 5.1932399029 0.7363810034
natoms 18; C 0 -0.9646559151 5.4733729248 -0.1597028646
natoms 19; H 0 -1.7219855447 4.4659706776 1.5196152522
natoms 20; C 0 -1.1205028345 6.4439581901 -1.3017332808
natoms 21; H 0 -0.5878374243 7.3791689974 -1.0895447428
natoms 22; H 0 -2.1633643356 6.6885000801 -1.5114185429
natoms 23; H 0 -0.6773725103 6.0136211229 -2.2034914048
natoms 24; C 0 0.3925942341 4.8015542942 -0.123885055
natoms 25; O 0 0.5701526599 4.0082477346 -1.3161765033
natoms 26; H 0 1.159685222 5.5805888878 -0.221070056
natoms 27; H 0 -0.1594803496 3.3619454132 -1.3119241367
natoms 28; C 0 0.7061641267 3.9672018553 1.108390936
natoms 29; H 0 0.0079139926 3.12941915 1.2017264863
natoms 30; H 0 0.655241531 4.5638492377 2.0234151234
natoms 31; H 0 1.7135259122 3.5570838627 1.0077387138
Variables:
   1 C -3.322 5.757 0.755
   2 C -4.334 4.780 0.125
   3 H -3.609 5.963 1.793
   4 H -3.375 6.712 0.222
   5 H -4.291 3.826 0.671
   6 H -4.017 4.570 -0.904
   7 C -5.746 5.309 0.128
   8 C -6.373 5.476 1.489
   9 H -5.953 6.339 2.019
  10 H -6.174 4.593 2.106
  11 H -7.454 5.612 1.440
  12 C -6.348 5.623 -1.035
  13 C -7.721 6.190 -1.244
  14 H -5.781 5.450 -1.951
  15 H -7.663 7.153 -1.765
  16 H -8.258 6.353 -0.309
  17 H -8.326 5.526 -1.871
  18 C -1.931 5.193 0.736
  19 C -0.965 5.473 -0.160
  20 H -1.722 4.466 1.520
  21 C -1.121 6.444 -1.302
  22 H -0.588 7.379 -1.090
  23 H -2.163 6.689 -1.511
  24 H -0.677 6.014 -2.203
  25 C 0.393 4.802 -0.124
  26 O 0.570 4.008 -1.316
  27 H 1.160 5.581 -0.221
  28 H -0.159 3.362 -1.312
  29 C 0.706 3.967 1.108
  30 H 0.008 3.129 1.202
  31 H 0.655 4.564 2.023
  32 H 1.714 3.557 1.008
QMtool: Assign unique names for all atoms:
Aliased name C --> C1
Aliased name C --> C2
Aliased name H --> H3
Aliased name H --> H4
Aliased name H --> H5
Aliased name H --> H6
Aliased name C --> C7
Aliased name C --> C8
Aliased name H --> H9
Aliased name H --> H10
Aliased name H --> H11
Aliased name C --> C12
Aliased name C --> C13
Aliased name H --> H14
Aliased name H --> H15
Aliased name H --> H16
Aliased name H --> H17
Aliased name C --> C18
Aliased name C --> C19
Aliased name H --> H20
Aliased name C --> C21
Aliased name H --> H22
Aliased name H --> H23
Aliased name H --> H24
Aliased name C --> C25
Aliased name O --> O26
Aliased name H --> H27
Aliased name H --> H28
Aliased name C --> C29
Aliased name H --> H30
Aliased name H --> H31
Aliased name H --> H32

Read 1 ModRedundant lines
Reading internal coordinates from 'Initial Parameters'.
Replacing current cartesian coordinates by coordinates from 'Input Orientation'.
Reading Mulliken charges.
Dipole moment: -1.4949 0.0664 1.3274
Reading ESP charges.
ESP charges not found!
Reading NPA charges.
NPA charges not found!
Loading cartesians as autogenerated new molecule C:/Users/Stefane/Desktop/Structure_Anja/Opt_cofactor/CHW_Part/CHW_Tail/Bond_Optim/CHW_Tail_hess_qmtool_tmp.pdb
0: SCF = -503.008413 hart = -315431.674595 kcal/mol; rel = 0.0000 kcal/mol
 Temperature 298.150 Kelvin. Pressure 1.00000 Atm.

****************************************************************
********************* Thermochemistry **********************
********************* **********************
****************************************************************

Gas phase:
================================================================
Eletronic energy E(vacuum) = -316655.05 Kcal/mol
Zero-point energy ZPE = 184.78 Kcal/mol
Internal energy U(298.150K) = 194.57 Kcal/mol
Enthalpy H(298.150K) = 195.17 Kcal/mol
Entropic term T*S = 38.57 Kcal/mol
Gibbs free energy G(298.150K) = 156.60 Kcal/mol
E(vacuum) + ZPE = -316470.27 Kcal/mol
E(vacuum) + U(298.150K) = -316460.48 Kcal/mol
E(vacuum) + H(298.150K) = -316459.89 Kcal/mol
E(vacuum) + G(298.150K) = -316498.46 Kcal/mol
Entropy S = 0.13 Kcal/(mol*K)
Heat capacity CV = 55.25 Cal/(mol*K)

****************************************************************
****************************************************************

internal hessian size = 155
Cartesian hessian size = 96
Force constant scaling factor=0.889249 for MP2
Harmonic frequencies: 90 (0 imaginary)
Creating namespace ::Optimize::Opt4

****************************************************************
****************************************************************

For the calculations with NAMD I have downloaded the last and correct version (I think) of the NAMD binary for Windows 7 64 bits from the Biocore website (the header message says version NAMD2.10 for windows multicore, built Dec 9th, 2014). Moreover If I execute NAMD directly (without a confile), the program starts normally the header says only 1 nodes and 1 core are used.

Since I am new with NAMD it is difficult to me to resolve this problem myself, so could you help me?

Thanks

Stéphane