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

[聂雪川]

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 > 
> |
> -----------------------------------------------------------