[gmx-users] Re: Problem of reading the atom'force from trr file using template.c

[Sebastian Waltz]

Hi Chuan,

in the template.c file is in the beginning the flag
initialized:

int        flags = TRX_READ_X;

If you want to read out the forces you have to change this
to, as:

int        flags = TRX_READ_F;

in addition to changing fr.x to fr.f.

Basti 

On Wed, 23 Jun 2010 20:00:27 +0800
 聂雪川 <niexuechuan at 163.com> wrote:
> Dear Mark ;
> The ./template dosn't have additional flags as shows
> below.The "-force" option dosn't work.
> 
>
==============================================================
> =Option     Filename  Type         Description
>
=------------------------------------------------------------
> =  -s         md.tpr  Input        Structure+mass(db):
> tpr tpb tpa gro g96 pdb
> =  -f         md.xtc  Input        Trajectory: xtc trr
> trj gro g96 pdb cpt
> =
> =Option       Type   Value   Description
> =------------------------------------------------------
> =-[no]h       bool   no      Print help info and quit
> =-nice        int    0       Set the nicelevel
> =-b           time   0       First frame (ps) to read
> from trajectory
> =-e           time   10      Last frame (ps) to read from
> trajectory
> =-dt          time   0       Only use frame when t MOD dt
> = first time (ps)
> =-[no]w       bool   no      View output xvg, xpm, eps
> and pdb files
> =-n           int    1       Plot data for atom number n
> (starting on 1)
>
===========================================================
> Chuan
> 
> > Date: Wed, 23 Jun 2010 18:40:36 +1000
> > From: Mark Abraham <mark.abraham at anu.edu.au>
> >  
> > You need to supply a trajectory that has forces, and
> then make the program read the forces (probably with
> -force on the command line). Alternatively, work through
> how the trajectory reading code works, and see how to set
> the flags to make them read forces.
> > 
> > Mark
> > 
> > ----- Original Message -----
> > From: è,é>ªå· <niexuechuan at 163.com>
> > Date: Wednesday, June 23, 2010 18:29
> > Subject: [gmx-users] Problem of reading the atom'force
> from trr file using template.c
> > To: gmx-users at gromacs.org
> > 
> > 
> >
>
   -----------------------------------------------------------
> >>> Dear all,
> >>    I am  trying  to analysis the force of a atom.So I
> change "fr.x[n][XX]" to  "fr.f[n][XX]" in the template.c
> .But it turns up "Segmentation fault" .(The  pointer
> "fr.f" is NULL) How could I get the force?
> > >   > My mdp file:
>  >   > title                =   Yo
> >> cpp                  =   /usr/bin/cpp
> >> constraints          =   all-bonds
> >> integrator           =   md
> >> dt                   =  0.002 ; ps  !
> >> nsteps               =  2500000 ; total 5ns.
> >> comm_mode     =  NonE
> >> nstcomm              =   
> >> nstxout              =   50
> >> nstvout              =   0
> >> nstfout              =   50
> >> nstxtcout            =   0 
> >> nstlog               =   5000
> >> nstenergy            =   5000
> >> nstlist              =   10
> >> ns_type              =   grid
> >> coulombtype           =PME
> >> rlist                =   1.4
> >> rcoulomb             =   1.4
> >> rvdw                 =   1.4
> >> pbc                  =  xyz
> >> ; Berendsen temperature coupling is on in two  groups
> >> Tcoupl               =   berendsen
> >> tc-grps              =  CNT  SOL 
> >> tau_t                =  0.1 0.1  > ref_t
>                =  300 300 
> >> ; Energy  monitoring
> >> energygrps           =  CNT SOL
> >> ; Non-equilibrium MD >   > freezegrps      = CNP  
> >> freezedim     =  Y Y  Y    
> >> ; Isotropic pressure coupling is now  on
> >> Pcoupl               =  no
> >> ;Pcoupltype           =  isotropic
> >> ;tau_p                =  0.5
> >> ;compressibility     =   4.5e-5
> >> ;ref_p                =  1.0
> >> ; Generate velocites is off at 300  K.
> >> gen_vel              =   no
> >> gen_temp             =   300.0
> >> gen_seed             =  537129 
> 
> >   >   > Many thanks in advance,
> >> Chuan > 
> > |
> >
>
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