[gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories
Justin Lemkul
jalemkul at vt.edu
Mon Aug 24 23:21:13 CEST 2015
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
>>
>> ==================================================
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--
==================================================
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
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