[gmx-users] Number of Frames in Trajectory

[Mark Abraham]

varsha gautham wrote:
> Dear users,
> 
> Am trying to simulate a polymer in vaccum.But when i make the production 
> run and view trajectory(.trr) files in VMD am getting only one 
> frame.Here's a part of my mdp file:
> 
> title               =  polymer
> cpp                 =  /lib/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.005    ;
> nsteps              =  50000    ;
> nstcomm             =  1
> nstxout             =  1000
> nstvout             =  1000
> nstfout             =  1000

Are you sure you want positions, velocities and forces every thousand 
steps? What are you going to do with the latter two? Check out the 
manual, chapter 7.

> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tau_t               =  0.1           0.1
> tc-grps            =  BEN           NCH0
> ref_t               =  300           300
> ; Pressure coupling is not on
> Pcoupl              =  no
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> 
> But the mdrun given for equilibriation step generated 96 frames.Is that 

Not possible - the above would generate at most 50.

> because of the algorithm that i specified in the integrtaor as 
> MD.Because other than md,when i gave bd or steep am getting more 
> frames.So what is the problem in obtining frames with  "md" as input for 
> integrator?

MD does MD, not energy minimization, as those others do.

Mark