[gmx-users] Re:gmx-users Digest, Vol 84, Issue 207

[Mark Abraham]

On 4/27/2011 11:52 AM, MD wrote:
> Hi Justin,
>
> When i define
>
> define =  FLEXIBLE

This is not of the correct form.

>   constraints = none
>   constraint-algorithm = Lincs
>
>
> I saw my .log file.
>
> Input Parameters:
> integrator = md
> nsteps = 10000
> init_step = 0
> ns_type = Grid
> nstlist = 5
> ndelta = 2
> nstcomm = 1
> comm_mode = Linear
> nstlog = 50
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstenergy = 50
> nstxtcout = 50
> init_t = 0
> delta_t = 0.002
> xtcprec = 1000
> nkx = 0
> nky = 0
> nkz = 0
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Berendsen
> epc = Berendsen
> epctype = Isotropic
> tau_p = 0.5
> ref_p (3x3):
> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> compress (3x3):
> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
> refcoord_scaling = No
> posres_com (3):
> posres_com[0]= 0.00000e+00
> posres_com[1]= 0.00000e+00
> posres_com[2]= 0.00000e+00
> posres_comB (3):
> posres_comB[0]= 0.00000e+00
> posres_comB[1]= 0.00000e+00
> posres_comB[2]= 0.00000e+00
> andersen_seed = 815131
> rlist = 0.9
> rtpi = 0.05
> coulombtype = Cut-off
> rcoulomb_switch = 0
> rcoulomb = 0.9Input Parameters:
> integrator = md
> nsteps = 10000
> init_step = 0
> ns_type = Grid
> nstlist = 5
> ndelta = 2
> nstcomm = 1
> comm_mode = Linear
> nstlog = 50
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstenergy = 50
> nstxtcout = 50
> init_t = 0
> delta_t = 0.002
> xtcprec = 1000
> nkx = 0
> nky = 0
> nkz = 0
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Berendsen
> epc = Berendsen
> epctype = Isotropic
> tau_p = 0.5
> ref_p (3x3):
> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> compress (3x3):
> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
> refcoord_scaling = No
> posres_com (3):
> posres_com[0]= 0.00000e+00
> posres_com[1]= 0.00000e+00
> posres_com[2]= 0.00000e+00
> posres_comB (3):
> posres_comB[0]= 0.00000e+00
> posres_comB[1]= 0.00000e+00
> posres_comB[2]= 0.00000e+00
> andersen_seed = 815131
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 0.9
> epsilon_r = 1
> epsilon_rf = 1
> tabext = 1
> implicit_solvent = No
> gb_algorithm = Still
> gb_epsilon_solvent = 80
> nstgbradii = 1
> rgbradii = 2
> gb_saltconc = 0
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> sa_surface_tension = 2.092
> DispCorr = EnerPres
> free_energy = no
> init_lambda = 0
> sc_alpha = 0
> sc_power = 0
> sc_sigma = 0.3
> delta_lambda = 0
> nwall = 0
> wall_type = 9-3
> wall_atomtype[0] = -1
> wall_atomtype[1] = -1
> wall_density[0] = 0
> wall_density[1] = 0
> wall_ewald_zfac = 3
> pull = no
> disre = No
> 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
> em_stepsize = 0.01
> em_tol = 100
> niter = 20
> fc_stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake_tol = 0.0001
> 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: 1941
> ref_t: 300
> tau_t: 0.1
> 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
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw: FALSE
> Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9
> System total charge: 0.000
>
> Enabling SPC water optimization for 216 molecules.
>
> Configuring nonbonded kernels...
> Testing AMD 3DNow support... not present.
> Testing ia32 SSE support... present.
>
>
>
>
>
>
>
>
>
>
>
>
>
> However if i
> define =
>
> constraints = none
> constraint-algorithm = Lincs
>
> The .log file is similar to the above .log file. So i can not know whether the constraints invoked.

I think you haven't looked far enough. Algorithms being used that are 
important enough to have names and literature citations are referred to 
by those in the .log file. Read and learn :-)

> Is it only SETTLE algorithm for water models in Gromacs 4.5.3?

Have you looked in the manual?

Mark

> >
> >
> >MD wrote:
> >>  Hi gromacs experts,
> >>
> >>  I used gromacs 4.5.3. my system has only spce water, no other types.
> >>
> >>  In .mdp file,
> >>
> >>  I used the following parameters;
> >>
> >>  define =
> >>
> >>  constraints = none
> >>  constraint-algorithm = Lincs
> >>
> >>  Can u tell me  Is it flexible water or all the bond, angle fixed using
> >>  the above setting?
> >>
> >
> >Look at spce.itp and/or your md.log file.  If the #ifdef FLEXIBLE statement is
> >not invoked, the SETTLE algorithm is used.
> >
> >>
> >>  what is the equations of potential energy in Gromacs 4.5 using OPLSAA?
> >>
> >
> >The components of various functional forms are described in the manual.
> >
> >-Justin
> >
> >>
> >>  Best regards
> >>
>
>
> ------------------------------------------------------------------------
> ÌåÑéÍøÒ×ÓÊÏä2G³¬´ó¸½¼þ£¬ÇáËÉ·¢ÓÅÖÊ´óµçÓ°¡¢´óÕÕƬ£¬ÌáËÙ3±¶! 
> <http://mail.163.com/html/110414_attachment/att1.htm> 




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110427/c4f63e73/attachment.html>