[gmx-users] testing Tip5p water

tuyusong tuyusong at gmail.com
Tue Sep 2 20:19:16 CEST 2008


Dear all,

         

         a similar problem was proposed in this list in 2002:

 http://www.gromacs.org/pipermail/gmx-users/2002-August/002339.html

I cannot solve my problem, when testing tip5p in gromacs. 

 

T( c)      density((g/cm^3)      -E(kcal/mol)  

REF1        25.0       0.999                   9.8676 

         REF2        25.0       0.984                  9.682

         my results   25.0       0.984                  -7.907

         (data published (REF1:JCP 112, p8910 (2000)),

 REF2: J. Chem. Phys. 117(19):8892-8897. (2002)) )

         I want to what results in the big difference above. 

 

         my main parameters:

a.            512 water molecules in NVT system from 1ns average collections
after 1ns equilibrium.

integrator               = md

dt                       = 0.001

nstlist                  = 10

ns_type                  = grid

 

pbc                      = xyz

rlist                    = 1

coulombtype              = PME 

rcoulomb                 = 1.0 

vdwtype                  = cut-off

rvdw                     = 1.22

 

DispCorr                 = Ener ;

fourierspacing           = 0.12

pme_order                = 6

Tcoupl                   = Berendsen

tau_t                    = 0.5

ref_t                    = 298

  

         Thanks a lot in advance!

 

 

Yusong

 

 

//////////////////////////////////////////////////////////////////////////

PS: here is md0.log:

CPU=  0, lastcg=  127, targetcg=  383, myshift=    2

CPU=  1, lastcg=  255, targetcg=  511, myshift=    2

CPU=  2, lastcg=  383, targetcg=  128, myshift=    2

CPU=  3, lastcg=  511, targetcg=  256, myshift=    2

nsb->shift =   2, nsb->bshift=  0

Listing Scalars

nsb->nodeid:         0

nsb->nnodes:      4

nsb->cgtotal:   512

nsb->natoms:   2560

nsb->shift:       2

nsb->bshift:      0

Nodeid   index  homenr  cgload  workload

     0       0     640     128       128

     1     640     640     256       256

     2    1280     640     384       384

     3    1920     640     512       512

 

parameters of the run:

   integrator           = md

   nsteps               = 1000000

   init_step            = 0

   ns_type              = Grid

   nstlist              = 10

   ndelta               = 2

   bDomDecomp           = FALSE

   decomp_dir           = 0

   nstcomm              = 1

   comm_mode            = Linear

   nstcheckpoint        = 1000

   nstlog               = 1500

   nstxout              = 250

   nstvout              = 250

   nstfout              = 250

   nstenergy            = 250

   nstxtcout            = 1000

   init_t               = 0

   delta_t              = 0.001

   xtcprec              = 1000

   nkx                  = 24

   nky                  = 24

   nkz                  = 21

   pme_order            = 6

   ewald_rtol           = 1e-05

   ewald_geometry       = 0

   epsilon_surface      = 0

   optimize_fft         = TRUE

   ePBC                 = xyz

   bUncStart            = FALSE

   bShakeSOR            = FALSE

   etc                  = Berendsen

   epc                  = No

   epctype              = Isotropic

   tau_p                = 1

   ref_p (3x3):

      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

   compress (3x3):

      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

   andersen_seed        = 815131

   rlist                = 1

   coulombtype          = PME

   rcoulomb_switch      = 0

   rcoulomb             = 1

   vdwtype              = Cut-off

   rvdw_switch          = 0

   rvdw                 = 1.22

   epsilon_r            = 1

   epsilon_rf           = 1

   tabext               = 1

   gb_algorithm         = Still

   nstgbradii           = 1

   rgbradii             = 2

   gb_saltconc          = 0

   implicit_solvent     = No

   DispCorr             = Ener

   fudgeQQ              = 0.5

   free_energy          = no

   init_lambda          = 0

   sc_alpha             = 0

   sc_power             = 0

   sc_sigma             = 0.3

   delta_lambda         = 0

   disre_weighting      = Conservative

   disre_mixed          = FALSE

   dr_fc                = 1000

   dr_tau               = 0

   nstdisreout          = 100

   orires_fc            = 0

   orires_tau           = 0

   nstorireout          = 100

   dihre-fc             = 1000

   dihre-tau            = 0

   nstdihreout          = 100

   em_stepsize          = 0.01

   em_tol               = 10

   niter                = 20

   fc_stepsize          = 0

   nstcgsteep           = 1000

   nbfgscorr            = 10

   ConstAlg             = Lincs

   shake_tol            = 1e-04

   lincs_order          = 4

   lincs_warnangle      = 30

   lincs_iter           = 1

   bd_fric              = 0

   ld_seed              = 1993

   cos_accel            = 0

   deform (3x3):

      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

   userint1             = 0

   userint2             = 0

   userint3             = 0

   userint4             = 0

   userreal1            = 0

   userreal2            = 0

   userreal3            = 0

   userreal4            = 0

grpopts:

   nrdf:                3069

   ref_t:                298

   tau_t:                0.5

anneal:                   No

ann_npoints:               0

   acc:            0           0           0

   nfreeze:           N           N           N

   energygrp_flags[  0]: 0

   efield-x:

      n = 0

   efield-xt:

      n = 0

   efield-y:

      n = 0

   efield-yt:

      n = 0

   efield-z:

      n = 0

   efield-zt:

      n = 0

   bQMMM                = FALSE

   QMconstraints        = 0

   QMMMscheme           = 0

   scalefactor          = 1

qm_opts:

   ngQM                 = 0

Max number of connections per atom is 4

Total number of connections is 1536

Max number of graph edges per atom is 4

Total number of graph edges is 1024

Table routines are used for coulomb: TRUE

Table routines are used for vdw:     FALSE

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald

Cut-off's:   NS: 1   Coulomb: 1   LJ: 1.22

System total charge: 0.000

Generated table with 1110 data points for Ewald.

Tabscale = 500 points/nm

Generated table with 1110 data points for LJ6.

Tabscale = 500 points/nm

Generated table with 1110 data points for LJ12.

Tabscale = 500 points/nm

Will do PME sum in reciprocal space.

 

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 

A smooth particle mesh Ewald method

J. Chem. Phys. 103 (1995) pp. 8577-8592

-------- -------- --- Thank You --- -------- --------

 

Parallelized PME sum used.

PARALLEL FFT DATA:

   local_nx:                   6  local_x_start:                   0

   local_ny_after_transpose:   6  local_y_start_after_transpose    0

Removing pbc first time

Done rmpbc

Center of mass motion removal mode is Linear

We have the following groups for center of mass motion removal:

  0:  System, initial mass: 9223.92

There are: 384 Atoms

There are: 256 VSites       

         

---

 P.O.800-204 Haiping Fang Group  

 Shanghai Institute of Applied Physics

 Chinese Academy of Sciences, China (201800)  

 

 Send email to:  <mailto:tuyusong at gmail.com> tuyusong at gmail.com

 Tel: (int : +86 21 59554533), (loc : 21 59554533)

 

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