[gmx-users] constraint pull code / gromacs 5.0.4

[Alex]

The pulling rate, as it appears in your mdp, is actually zero. That aside,
we do not have enough info about the system. What are the nanoparticles
made of? What forcefield is being used? Can you use trjconv to see what's
going on?
Please check that your system is happy prior to pulling. The huge variation
in forces could mean weird pulling behavior (which does happen), or that
your particles are "breathing." Set constraints to 'none' and pull code to
see if your system behaves. The use of constraints should be deprecated in
general, but I fear for my life suggesting it here.

Alex

On Tue, Jun 23, 2015 at 11:53 AM, CARDELLINI ANNALISA <d021974 at polito.it>
wrote:

> Dear gromacs users,
> I'm using the pull code to evaluate the Potential of Mean Forces between
> two nanoparticles(NPs) of Radius = 1nm.
> Specifically, in order to create the configurations (i.e.the 2 NPs at
> different centr of mass distance) I used the constraint pull code.
> Then for each configuration I run a simulation of 2ns. Part of the mdp
> file that I used is:
> ...
> ; 9) NEIGHBOR SEARCHING
> ; cut-off scheme
> cutoff-scheme       = Verlet
> nstlist             =  10    ;
> ns_type             =  grid
> pbc        =  xyz
> periodic_molecules  =  yes
> rlist               =  1.3     ;
>
> ; 10) ELECTROSTATICS
> coulombtype         =  PME-Switch   ;
> pme_order           =  4
> rcoulomb            =  1.3     ;
> rcoulomb-switch     =  1.25     ;
>
> ; 11) VdW
> vdw-type            =  Cut-off  ;
> rvdw-switch         =  1.3      ;
> rvdw                =  1.3
> DispCorr            =  EnerPres ;
>
> ; 13) EWALD
> fourierspacing      =  0.12  ; (0.12) [nm] default
> fourier_nx          =  0     ; (0) default
> fourier_ny          =  0     ; (0) default
> fourier_nz          =  0     ; (0) default
> ewald_rtol          =  1e-5  ; (1e-5) default
> optimize_fft        =  yes
>
> ; 14) TEMPERATURE COUPLING
> Tcoupl                  = Nose-Hoover
> tc_grps                 = UNK        SOL
> tau_t                   = 0.1        0.1
> ref_t                   = 300        300
>
> ; 15) PRESSURE COUPLING
> Pcoupl              =  Parrinello-Rahman
> Pcoupltype          =  isotropic
> tau_p               =  2       2        ; (1) [ps] default
> compressibility     =  4.5e-5  4.5e-5   ; [bar-1]
> ref_p               =  1    1    ; [bar]
> refcoord_scaling    =  com    ;
>
> ; 17) VELOCITY GENERATION
> gen-vel                  = no
> gen-temp                 = 300
> gen-seed                 = -1
>
> ; 18) BONDS
> constraints             = ; convert all bonds to constraints
> constraint_algorithm    = ; LINear Constraint Solver
> continuation            = yes           ;
> lincs_order             = 4             ;
> lincs_iter              = 1             ;
> lincs_warnangle         = 90            ;
>
> ; Pull type:
> pull                     = constraint                    ;
> pull-geometry            = distance                      ;
> pull-dim                 = Y N N                         ;
> pull-start               = yes                           ;
> pull-ngroups             = 2                             ;
> pull-group1-name         = 1UNK                          ;
> pull-group2-name         = 2UNK
> pull-coord1-groups       = 1 2
> pull-coord1-rate         = 0.0                           ; 0.01 nm per ps
> pull-nstxout             = 1000      ; every 2 ps
> pull-nstfout             = 1000      ; every 2 ps
> pull-coord1-init         = 0.0       ;
>
> My problem is related to the resulting forces that I obtained. They do not
> seem to converge and they are really fluactuating for any configuration
> (i.e. indipendently from the com distance)
> An example of pullf.xvg that I obtained at 2 nm com distance
> ..
> 1992.5000       -2367.46
> 1993.0000       -6738.59
> 1993.5000       361.472
> 1994.0000       647.644
> 1994.5000       -6222.61
> 1995.0000       6018.37
> 1995.5000       1921.95
> 1996.0000       -1618.72
> 1996.5000       1279.2
> 1997.0000       1302.08
> 1997.5000       2256.82
> 1998.0000       1485.05
> 1998.5000       2318.51
> 1999.0000       -3588.26
> 1999.5000       979.835
> 2000.0000       -678.607
>
> Of course, the PMF that I got with a simple intagration of the forces is
> characterized by enormous error bars and its shape does not have any sense.
>
> Do you have some suggestions for getting converged forces? Do you see some
> errors in the mdp file?
> Thank you in advance for your help.
> Annalisa
>
>
>
> Annalisa Cardellini, M.Sc.
> Ph.D. student
>
> Politecnico di Torino - Energy Department
> Corso Duca degli Abruzzi, 24
> 10129 Turin - ITALY
> Tel: +39-011-090-4495
> Fax: +39-011-090-4499
>
> E-mail: annalisa.cardellini at polito.it
> SMaLL: http://www.polito.it/small
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