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 <jalem...@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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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