[gmx-users] constraint pull code / gromacs 5.0.4

CARDELLINI ANNALISA d021974 at polito.it
Wed Jun 24 14:53:20 CEST 2015


Dear Alex,
thank you for your email.

> The pulling rate, as it appears in your mdp, is actually 
>zero.
That mdp file was related to one single window, after 
having pulling one particle apart from the other one.

> we do not have enough info about the system. What are 
>the nanoparticles
> made of?
My nanoparticles (Radius = 1nm) are made of alumina and 
the force field was CLAYFF


>Can you use 
>trjconv to see what's
> going on?
> Please check that your system is happy prior to pulling. 
The pulling step should be ok. I checked the positions of 
the COM nanoparticles and they were exactly where I 
expected from the pull rate and time step.

I have already evaluated the PMF with the harmonic 
potential (pull = umbrella) but the results were strong 
dependently from the k (spring constant) and I did not 
understand the right method to choose "k"

Thank you very much for your answer
Annalisa




On Tue, 23 Jun 2015 12:10:57 -0600
  Alex <nedomacho at gmail.com> wrote:
> 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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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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