Sarah Witzke wrote:
Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole
Sendt: fr 05-06-2009 13:32
Til: Discussion list for GROMACS users
Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd
Sarah Witzke wrote:
Dear XAvier,
Thank you very much for your answer. I have posted my .mdp file in the bottom
of the email - as I haven't specified comm_mode or nstcomm, the default values
should be used -
this is also confirmed in the .log file:
nstcomm = 1
comm_mode = Linear
For bilayer systems it is often recommended to removed the solvent and
bilayer separately,
they may move in opposite directions and also you remove the COM of the
system the
solvent and bilayer might move on relative to the other.
Thank you very much for telling me that. I'm sorry to ask, but how can you can
you remove motion for the bilayer separately from the solvent?
Use comm-grps and carefully-designed index groups.
-Justin
This should be fine, right? I have indeed removed the overall COM motion for
each step of the simulation?
Just to be sure: To convert the .trr file to an .xtc I could use this command:
trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s
dmpclim32-1.tpr -o dmpclim32-all.xtc
I should not use -center (is that redundant when having nstcomm and comm_mode
in the .mdp file?) or -fit rot+trans? Would your advice be to use -pbc nojump
or just not -pbc at all? One last question: What is really the difference
between -pbc nojumb and whole?
No, you just feed g_msd the trajectory trr the way it is. Or convert it
in xtc if you like.
You have to monitor the COM of the bilayer to check that the COM is
indeed removed. For this you can do:
1) trjconv -f traj.trr -pbc nojump -o traj-nojump.xtc
2) g_traj -f traj-nojump.xtc -com -ox coord-COM.xvg -n index.ndx; in
that step you choose the bilayer
in your index and get the coordinates of the COM for which you can
monitor the x, y and z values.
Oh, I'm sorry to have written my last email to fast, I meant to erase -center,
-fit, and -pbc from the command :-(
I'll try your suggestions with trjconv and g_traj.
I looked at g_msd -h for version 4.0.2, 4.0.3, and 4.0.4 (I'm using 4.0.4) and
they all had the -rmcomm option, the manual version 3.3 doesn't mention it
however.
I was referring to the versions prior 4.0.X. It might be good to use it,
it is definitely
necessary to remove it.
Thank you,
Sarah
#################.mdp file#############
title = DMPC-LIM bilayer, 1 LIM and 128 lipids
cpp = /lib/cpp
integrator = md
dt = 0.002 ; ps
tinit = 0
init_step = 5000
nsteps = 75000000
;-------------------------
; Bond constraints
define = ; posres etc.
constraints = all-bonds ; constrain all bond lengths
constraint_algorithm = lincs ; default
lincs_order = 4 ; default
; X/V/F/E outputs
nstxout = 5000 ; pos out --- 10 ps
nstvout = 5000 ; vel out --- 10 ps
nstfout = 0 ; force out --- no
;nstlog = 5000 ; energies to log (0.5 ps)
nstenergy = 5000 ; energies to energy gile
; Neighbour list
ns_type = grid ; neighlist type
nstlist = 10 ; Freq. to update neighbour list
rlist = 1.0 ; nm (cutoff for short-range NL)
; Coulomb interactions
coulombtype = PME ; Particle Mesh Ewald
rcoulomb = 1.0 ; nm (direct space sum cut-off)
optimize_fft = yes ; optimal FFT plan for the grid
; van der Waals interactions
vdwtype = Cut-off ; Van der Waals interactions
rvdw = 1.0 ; nm (LJ cut-off)
; Temperature coupling
Tcoupl = berendsen
tc-grps = DMPC LIM_SOL
tau_t = 0.1 0.1 ; ps
ref_t = 310 310 ; K
; Energy monitoring
energygrps = DMPC LIM_SOL
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = semiisotropic ; semi: (xy) and (z) separately
tau_p = 1.0 1.0 ; ps
compressibility = 4.5e-5 4.5e-5 ; 1/bar (water @ 1 atm, 300 K)
ref_p = 1.0 1.0 ; bar
#####################################
________________________________
Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole
Sendt: fr 05-06-2009 09:34
Til: Discussion list for GROMACS users
Emne: Re: [gmx-users] diffusion coefficient with g_msd
On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote:
Dear gromacs users,
I have done several simulations with small lipophilic, molecules
diffusing into a DMPC bilayer.
I would like to calculate the diffusion coefficient of the molecules
inside the membrane, and therefore I looked at g_msd. The manual
(version 4.0) states on p. 250 (manual pages) that g_msd uses the
Einstein relation. Reading "Molecular Modelling: principles and
applications" 2.ed. by Andrew Leach it is explained that the "for
calculating the diffusion coefficient the mean-squared distances
should not be limited by the edges of the periodic box. In other
words, we require a set of positions that have not been translated
back into the central simulation cell." This makes sense since I try
to calculate the distance a molecule diffuse.
I haven't been able to find any mention of how gromacs handle this
either in the manual or on the wiki page. The search function on the
old webpage directs me to the new webpage, which doesn't give any
results for "g_msd" or "diffusion coefficient" or alike, so my
apologies for asking a question I could have found the answer to I
old emails. When I google I get some of the old emails on g_msd from
the gromacs website, but I can only read some of them (the others
direct me to an empty page in the new webpage).
The first question is whether I can use my .xtc file made with this
command from the original .trr file:
trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc
whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc (for fitting and
centring the DMPC group is used)
I would guess I could not, but should I then do the command again
creating a new .xtc file, but without using -center and -pbc whole?
You are right. You can not use this trajectory. The fitting procedure
will alter the diffusion of the system overall.
If you had to do something it would be to use -pbc nojump to allow the
molecules to freely diffuse.
g_msd takes care of the periodicity of your system. So you do not have
to fit or anything.
My second question is why g_msd has the option -rmcomm to remove COM
motion? How is g_msd created so that the diffusion coefficient can
be calculated if COM motion is removed?
The removal of the center of mass of the ENTIRE system is necessary
before calculating the msd.
This is generally done during the run using options in the mdp file.
Which version you are using? I'd never seen the -rmcomm before? You
can try to determine your
msd with and without the option and see if it affects your result.
This would depend on the removal
or not of the COM motion in your simulation.
XAvier.
Thank you very much for your time,
Sarah
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--
----------------------------------
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel: +31-503634329
Fax: +31-503634398
email: x.peri...@rug.nl
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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