[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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