[gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories
Mark Abraham
mark.j.abraham at gmail.com
Tue Aug 25 11:16:44 CEST 2015
Hi,
Quick nitpick... Justin's right on the important points, but note that
mdrun -nt may (or may not) use domain decomposition depending on the .tpr
settings and the way GROMACS was configured. (e.g. a build with OpenMP and
thread-MPI is permitted to use either, and the latter triggers the use of
domain decomposition). Anu's observations are of single trajectories whose
behaviour is not expected to be reproducible.
Mark
On Mon, Aug 24, 2015 at 11:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/24/15 5:39 AM, anu chandra wrote:
> > Dear Justin
> >
> > Thanks for the reply.
> >
> > If that's the case what position of atoms the coordinates in trr file
> > represents?. If I got you right, the coordinates in trr file neither get
> > along with the mdrun generated gro file due to domain decomposition
> (hence
> > broken molecules) nor with the trjconv treated gro file since, as you
> said,
> > the same treatment with trjconv is required for coordinates in trr file.
> >
>
> I don't really understand the question, but the generic answer is: mdrun
> doesn't
> care about our visualization convenience. The physics don't depend on
> molecules
> being represented as "whole" so it does not waste time reconstructing them
> to
> write them to the trajectory. That's what trjconv is for - processing
> *any*
> trajectory or coordinate file that is "broken" across PBC. Your input
> coordinates were probably whole, so in order to visualize the trajectory,
> you
> need to use trjconv to process the .trr suitably. There are tips on the
> GROMACS
> website and in about half a million posts in the list archive on this.
>
> -Justin
>
> > Many thanks
> >
> > Anu
> >
> > On Wed, Aug 19, 2015 at 12:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 8/19/15 7:22 AM, anu chandra wrote:
> >>
> >>> Dear Gromacs users,
> >>>
> >>> I just noticed that during simulation 'mdrun' writes gro file in two
> >>> formats - one with broken molecules at the boundaries and other one
> where
> >>> surface molecules are perfectly wrapped. Interestingly, this
> difference in
> >>> format depends on where I run the simulation - either in a cluster or
> in
> >>> my
> >>> local 8-core desktop machine. Using 'mdrun' in cluster gives gro file
> with
> >>> broken molecules at the boundaries and my desktop workstation gives
> the
> >>> one with complete molecules at the surface. Below is the mdp file I
> used
> >>> for simulation in both case
> >>>
> >>>
> >>>
> *************************************************************************************
> >>>
> >>> define = -DPOSRES_MD
> >>> ;
> >>> integrator = md
> >>> dt = 0.002
> >>> nsteps = 50000
> >>> ;
> >>> nstlog = 1000
> >>> nstxout = 1000
> >>> nstvout = 1000
> >>> nstfout = 1000
> >>> nstcalcenergy = 100
> >>> nstenergy = 1000
> >>> ;
> >>> cutoff-scheme = Verlet
> >>> nstlist = 20
> >>> rlist = 1.2
> >>> coulombtype = pme
> >>> rcoulomb = 1.2
> >>> vdwtype = Cut-off
> >>> vdw-modifier = Force-switch
> >>> rvdw_switch = 1.0
> >>> rvdw = 1.2
> >>> ;
> >>> pbc = xyz
> >>> ;
> >>> tcoupl = Nose-Hoover
> >>> tc_grps = Protein POPC CL_SOL
> >>> tau_t = 0.5 0.5 0.5
> >>> ref_t = 305.0 305.0 305.0
> >>> ;
> >>> pcoupl = Parrinello-Rahman
> >>> pcoupltype = semiisotropic
> >>> tau_p = 5.0
> >>> compressibility = 4.5e-5 4.5e-5
> >>> ref_p = 1.0 1.0
> >>> ;
> >>> constraints = h-bonds
> >>> constraint_algorithm = LINCS
> >>> continuation = yes
> >>> ;
> >>> nstcomm = 100
> >>> comm_mode = linear
> >>> comm_grps = Protein_POPC CL_SOL
> >>> ;
> >>> refcoord_scaling = com
> >>> ***********************************************************************
> >>>
> >>> May I know what is making this difference? Due to the presence of
> broken
> >>> molecules, I failed to visualizing the trajectories (.trr file) using
> VMD.
> >>> Though I could make a gro file with complete molecules at the
> boundaries
> >>> using trjconv command,
> >>>
> >>>
> >>> *trjconv -f input.gro -o ouput.gro -s input.tpr -pbc mol*
> >>> the visualization of trr file with output.gro also shows long bond
> between
> >>> atoms across the boundaries. Please help me to rectify this issue with
> >>> visualizing the trr file.
> >>>
> >>>
> >> You need to process the .trr file the same way using trjconv.
> Accounting
> >> for periodicity effects is a routine first step after a run finishes.
> >>
> >
> >> In server, following grommp and mdrun commands are used,
> >>>
> >>>
> >>>
> >>> *gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb
> -n
> >>> index.ndx -p topol.topmpirun -ppn 16 -np 64 gmx_mpi mdrun -deffnm MD5*
> >>>
> >>>
> >> Here, you're using domain decomposition (anything > 8 cores). Broken
> >> molecules get written.
> >>
> >> and, in my desktop workstation following commands are used
> >>>
> >>>
> >>>
> >>> *gmx grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n
> >>> index.ndx -p topol.topgmx mdrun -nt 8 -deffnm MD5*
> >>>
> >>>
> >> Here, there is no DD. Molecules are whole.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list