[gmx-users] xtc file and trr file

[Acoot Brett]

Dear Justin,
 
But it is very difficult to explain why the xtc file gives more frames in VMD than trr file. Can you explain it? Or VMD has made the modification when read the xtc file or the trr file?
 
Cheers,
 
Acoot


----- Forwarded Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, 18 August 2012 7:39 AM
Subject: Re: [gmx-users] xtc file and trr file



On 8/17/12 4:33 PM, Acoot Brett wrote:
> Dear All,
>
> Follwong is the MD mdp file I used for my production MD, which I downloaded from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp.
> Clearly it writes how it extract xtp file. Will you please explain to me which is the command for the extraction of trr file? And based on which command we can know by VMD the xtc file will have more frames in comparison with the trr file?
>

The .trr file is the "normal" trajectory, .xtc is considered optional and is 
only written with a non-zero value of nstxtcout.  A .trr file is produced as 
long as one of nstxout, nstvout, or nstfout are non-zero.

You control output frequency with all of these keywords.  In this case, both the 
.xtc and .trr files will have the same number of frames, every 2 ps, which is 
usually far more frequent than you'd normally want.

-Justin

> Cheers,
>
> Acoot
>
>
> title        = OPLS Lysozyme MD
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 500000    ; 2 * 500000 = 1000 ps, 1 ns
> dt        = 0.002        ; 2 fs
> ; Output control
> nstxout        = 1000        ; save coordinates every 2 ps
> nstvout        = 1000        ; save velocities every 2 ps
> nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps
> nstenergy    = 1000        ; save energies every 2 ps
> nstlog        = 1000        ; update log file every 2 ps
> ; Bond parameters
> continuation    = yes        ; Restarting after NPT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = all-bonds    ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter    = 1        ; accuracy of LINCS
> lincs_order    = 4        ; also related to accuracy
> ; Neighborsearching
> ns_type        = grid        ; search neighboring grid cells
> nstlist        = 5        ; 10 fs
> rlist        = 1.0        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range electrostatics
> pme_order    = 4        ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = V-rescale    ; modified Berendsen thermostat
> tc-grps        = Protein Non-Protein    ; two coupling groups - more accurate
> tau_t        = 0.1    0.1    ; time constant, in ps
> ref_t        = 300     300    ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 2.0        ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
> compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
>
>
> ----- Forwarded Message -----
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Friday, 17 August 2012 8:41 PM
> Subject: Re: [gmx-users] xtc file and trr file
>
> On 17/08/2012 6:46 PM, Acoot Brett wrote:
>> Dear All,
>>
>> After a production MD, both the xtc file and trr file are produced. trr file is much larger than the xtc file. But when we openned the original gro file one of the file from xtc file and trr file in VMD, we will find the xtc contains more frames in comparison with the trr file.
>>
>> Will you please explain why xtc file is smaller file than the trr file, but the xtc file contains more frames in VMD?
>
> Clearly one format is more efficient at storing frames than the other. They have different numbers of frames because that's what you asked for in your .mdp file (unless you've post-processed).
>
> Mark
> -- gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
========================================

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

========================================