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

[Mark Abraham]

----- Original Message -----
From: 聂雪川 <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

 
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> 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?

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

 >   > 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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