[gmx-users] output force

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 10 19:40:02 CEST 2010



Петр Попов wrote:
> And what if I have four helices in Protein and a,b,c,d group for each 
> helix in index.file and I want to get a-c pmf?
> 

If you have these helices in index groups, then specify these groups in the 
energygrps setting.  The group concept is explained in the manual, as well as 
the use of index files.

-Justin

> 
> 10 октября 2010 г. 21:20 пользователь Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> написал:
> 
> 
> 
>     Justin A. Lemkul wrote:
> 
> 
> 
>         Петр Попов wrote:
> 
>             Unfortunately I've got an error.
> 
>             This is .mdp file:
> 
>             title = title
>             cpp                 =  /lib/cpp
>             integrator          =  md
>             tinit               =  0.0
>             dt                  =  0.002 nsteps              =  25000
>             nstcomm             =  1
>             comm_grps           =  System
>             ld_seed             =  -1
>             niter               =  40
>             nstxout             =  10000
>             nstvout             =  0
>             nstfout             =  0
>             nstlog              =  500
>             nstenergy           =  100
>             nstlist             =  10
> 
> 
>     If this .mdp file is to be used for a rerun, please recall the
>     advice I gave you earlier about the proper setting for nstlist.
> 
>     -Justin
> 
> 
>             ns_type             =  grid
>             rlist               =  1.2
>             coulombtype         =  PME
>             rcoulomb            =  1.2
>             fourierspacing      =  0.12
>             pme_order           =  4
>             optimize_fft        =  yes
>             pbc                 =  xyz
>             vdwtype             =  Cut-off
>             rvdw                =  1.2
>             tcoupl              =  V-rescale
>             tc_grps             =  System
>             tau_t               =  0.1
>             ref_t               =  300.0
>             annealing           = single
>             annealing_npoints   = 3
>             annealing_time      = 0 5 50
>             annealing_temp      = 5 300 300
>             pcoupl              =  berendsen
>             pcoupltype          =  isotropic
>             compressibility     =  4.5e-5
>             tau_p               =  10.0
>             ref_p               =  1.0
>             gen_vel             =  yes
>             gen_temp            =  5.0
>             gen_seed            =  -1
>             constraints         =  all-bonds
>             constraint_algorithm      =  Lincs
>             lincs_order         =  4
>             disre               =  simple
>             disre_weighting     = conservative
>             disre_mixed         = no
>             nstdisreout         = 50000
>             disre_tau           = 0
>             pull                = constraint
>             pull_geometry       = distance
>             pull_dim            = Y Y Y
>             pull_constr_tol     = 1e-6
>             pull_nstfout        = 1
>             pull_nstxout        = 1
>             pull_ngroups        = 1
>             pull_group0         = a
>             pull_group1         = b
>             pull_init1          = 0.700
>             pull_start          = no
>             pull_k1             = 1000
>             lincs_iter          = 2
>             energygrps          = Protein Protein
> 
>             I just replace in .mdp file line energygrps = System and the
>             error is:
> 
>             Fatal error:
>             Atom 1 in multiple Energy Mon. groups (1 and 2)
> 
>             What should I do to avoid this?
> 
> 
>         You cannot use multiple energygrps if those groups overlap in
>         any way, as the error indicates.  I thought you were setting
>         "energygrps = Protein SOL"?  If you're trying to get
>         protein-only terms, then just set "energygrps = Protein"
> 
>         -Justin
> 
> 
> 
>             10 октября 2010 г. 20:01 пользователь Петр Попов
>             <magistrpetrus at gmail.com <mailto:magistrpetrus at gmail.com>
>             <mailto:magistrpetrus at gmail.com
>             <mailto:magistrpetrus at gmail.com>>> написал:
> 
>                Thank you very much!
> 
>                10 октября 2010 г. 19:58 пользователь Justin A. Lemkul
>                <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> написал:
> 
> 
> 
>                    Петр Попов wrote:
> 
>                        So if I want to get protein-solvent component I
>             should add
>                        in .mdp:
> 
>                        energygrps = Protein SOL
> 
>                        ?
> 
> 
>                    Yes, and set nstlist = 1.
> 
>                    -Justin
> 
>                        10 октября 2010 г. 16:41 пользователь Justin A.
>             Lemkul
>                        <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                        <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> написал:
> 
> 
> 
> 
>                           Петр Попов wrote:
> 
>                               Thank you for response!
>                               One more question:
>                               How can I get file with energy groups?
>             Should I use
>                        grompp with
>                               a -e ener.edr option? In this case, how to
>             build
>                        ener.edr file?
> 
> 
>                           The "energrygrps" keyword is an .mdp option,
>             so generate
>                        a new .tpr
>                           file with the desired groups and use the
>             -rerun feature
>                        of mdrun on
>                           the trajectory that has already been produced.
> 
>                           -Justin
> 
>                               9 октября 2010 г. 14:50 пользователь Mark
>             Abraham
>                               <mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>
>                        <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>
>                        <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>
>                        <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>>
>                               <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>
>                        <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>
>                               <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>
>                        <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>>>> написал:
> 
> 
>                                  You can get that with cunning use of
>             energy groups
>                        and mdrun
>                               -rerun,
>                                  but not mid-simulation.
>                                  Mark
> 
>                                  ----- Original Message -----
>                                  From: Петр Попов
>             <magistrpetrus at gmail.com <mailto:magistrpetrus at gmail.com>
>                        <mailto:magistrpetrus at gmail.com
>             <mailto:magistrpetrus at gmail.com>>
>                               <mailto:magistrpetrus at gmail.com
>             <mailto:magistrpetrus at gmail.com>
>                        <mailto:magistrpetrus at gmail.com
>             <mailto:magistrpetrus at gmail.com>>>
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>             <mailto:magistrpetrus at gmail.com>>
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>             <mailto:magistrpetrus at gmail.com>
>                        <mailto:magistrpetrus at gmail.com
>             <mailto:magistrpetrus at gmail.com>>>>>
>                                  Date: Saturday, October 9, 2010 21:41
>                                  Subject: [gmx-users] output force
>                                  To: gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>
>                        <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>>
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>             <mailto:gmx-users at gromacs.org>>>>
> 
>                                   > Hello dear gmx-users!
>                                   >
>                                   > When calculated forces in gromacs to
>             produce
>                        pmf, we have
>                               the net
>                                  force in output. For example:
>                                   > ...
>                                   > #
>                                   > # Giving Russians Opium May Alter
>             Current Situation
>                                   > #
>                                   > @    title "Pull force"
>                                   > @    xaxis  label "Time (ps)"
>                                   > @    yaxis  label "Force (kJ/mol/nm)"
>                                   > @TYPE xy
>                                   > 0.000000                1017490.761270
>                                   > 0.002000                -253098.034916
>                                   > 0.004000                -43856.400160
>                                   > 0.006000                48980.619113
>                                   > 0.008000                52103.053067
>                                   > 0.010000                33788.090031
>                                   > 0.012000                19096.388350
>                                   > 0.014000                14094.738810
>                                   > 0.016000                14027.621966
>                                   > 0.018000                15162.993741
>                                   > 0.020000                14136.978177
>                                   > ... etc.
>                                   >
>                                   > What sould I do to get the net force of
>                        protein-solvent
>                                  interactions or protein-protein
>             interactions or
>                        solvent-solvent
>                                  interactions instead and get output
>             .xvg file in
>                        the form
>                               like this:
>                                   >
>                                   > time     Force(type1)  
>              Force(type2)               Force(type3)
>                                   >
>                                   > t1         f1                   f1  
>                                         f1
>                                   > t2         f2                   f2  
>                                         f2
>                                   > t3         f3                   f3  
>                                         f3
>                                   > ...        ...                   ...
>                                           ...
>                                   > etc.
>                                   >
>                                   > Thank you for attention and I hope
>             you will
>                        help me!
>                                   > --
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>                           --     ========================================
> 
>                           Justin A. Lemkul
>                           Ph.D. Candidate
>                           ICTAS Doctoral Scholar
>                           MILES-IGERT Trainee
>                           Department of Biochemistry
>                           Virginia Tech
>                           Blacksburg, VA
>                           jalemkul[at]vt.edu <http://vt.edu>
>             <http://vt.edu> <http://vt.edu> |
>                        (540) 231-9080
> 
>                          
>             http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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>                    --         ========================================
> 
>                    Justin A. Lemkul
>                    Ph.D. Candidate
>                    ICTAS Doctoral Scholar
>                    MILES-IGERT Trainee
>                    Department of Biochemistry
>                    Virginia Tech
>                    Blacksburg, VA
>                    jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
>             (540) 231-9080
>                    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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