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Hi Alex<br>
<br>
You're running just 1ns, which is actually too short for production
in this kind of systems. Enlarge the simulation time (e.g. up to
50ns) and see if you get a more reasonable Scd plots. <br>
<br>
Javier<br>
<br>
El 08/11/11 21:40, Alex Jemulin escribió:
<blockquote
cite="mid:1320784821.50177.YahooMailNeo@web132402.mail.ird.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div><span>Dear Javier<br>
<br>
Here is mdp file for MD run<br>
<br>
title = cxcr7-DPPC Production MD <br>
; <br>
Run parameters<br>
<br>
integrator = md ; leap-frog integrator<br>
<br>
nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)<br>
<br>
dt = 0.002 ; 2 fs<br>
; <br>
Output control<br>
<br>
nstxout = 1000 ; save coordinates every 2 ps<br>
<br>
nstvout = 1000 ; save velocities every 2 ps<br>
<br>
nstxtcout = 1000 ; xtc compressed trajectory
output every 2 ps<br>
<br>
nstenergy = 1000 ; save energies every 2 p<br>
<br>
nstlog = 1000 ; update log file every 2 ps<br>
<br>
; Bond parameters<br>
<br>
continuation = yes ; Restarting after NPT <br>
<br>
constraint_algorithm = lincs ; holonomic <br>
constraints <br>
constraints = all-bonds ; all bonds (even
heavy atom-H bonds) constrained<br>
<br>
lincs_iter = 1 ; accuracy of LINCS<br>
<br>
lincs_order = 4 ; also related to
accuracy<br>
<br>
; Neighborsearching<br>
<br>
ns_type = grid ; search neighboring grid cels<br>
<br>
nstlist = 5 ; 10 fs<br>
<br>
rlist = 1.2 ; short-range neighborlist cutoff
(in nm)<br>
<br>
rcoulomb = 1.2 ; short-range electrostatic cutoff
(in nm)<br>
<br>
rvdw = 1.2 ; short-range van der Waals cutoff
(in nm)<br>
; <br>
Electrostatics<br>
<br>
coulombtype = PME ; Particle Mesh Ewald for
long-range electrostatics<br>
<br>
pme_order = 4 ; cubic interpolation<br>
<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>
<br>
; Temperature coupling is on<br>
<br>
tcoupl = Nose-Hoover ; More accurate
thermostat<br>
<br>
tc-grps = Protein DPPC SOL_NA ; three coupling
groups - more accurate<br>
<br>
tau_t = 0.5 0.5 0.5 ; time constant,
in ps<br>
<br>
ref_t = 323 323 323 ; reference
temperature, one for each group, in K<br>
; <br>
Pressure coupling is on<br>
<br>
pcoupl = Parrinello-Rahman ; Pressure coupling
on in NPT<br>
<br>
pcoupltype = semiisotropic ; uniform scaling
of x-y box vectors, independent <br>
z<br>
tau_p = 2.0 ; time constant, in ps<br>
<br>
ref_p = 1.0 1.0 ; reference
pressure, x-y, z (in bar)<br>
<br>
compressibility = 4.5e-5 4.5e-5 ; isothermal
compressibility, bar^-1<br>
; <br>
Periodic boundary conditions<br>
<br>
pbc = xyz ; 3-D PBC<br>
; <br>
Dispersion correction<br>
<br>
DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; <br>
Velocity generation<br>
<br>
gen_vel = no ; Velocity generation is off<br>
<br>
; COM motion removal<br>
<br>
; These options remove motion of the protein/bilayer
relative to the solvent/ions<br>
<br>
nstcomm = 1<br>
<br>
comm-mode = Linear<br>
<br>
comm-grps = Protein_DPPC SOL_NA <br>
<br>
Here are some graphs I made after MD run:<br>
g_energy -f md_0_1.edr -o temperature_MD.xvg<br>
<a class="moz-txt-link-freetext" href="http://www.freeimagehosting.net/ca04e">http://www.freeimagehosting.net/ca04e</a><br>
<br>
g_energy -f md_0_1.edr -o pressione_MD.xvg<br>
<a class="moz-txt-link-freetext" href="http://www.freeimagehosting.net/d3387">http://www.freeimagehosting.net/d3387</a><br>
<br>
<br>
g_energy -f md_0_1.edr -o totenergia_MD.xvg<br>
<a class="moz-txt-link-freetext" href="http://www.freeimagehosting.net/108a7">http://www.freeimagehosting.net/108a7</a><br>
<br>
<br>
Here are commands for calculating deuterium order parameters<br>
<br>
make_ndx -f md_0_1.tpr -o sn1.ndx<br>
> a C34 <br>
> a C36 <br>
> a C37 <br>
> a C38 <br>
... <br>
> a C50 <br>
> del 0-21 <br>
> q <br>
<br>
g_order -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od
deuter_sn1.xvg<br>
<br>
make_ndx -f md_0_1.tpr -o sn2.ndx<br>
carbons C17-C31 <br>
del 0-21 <br>
q<br>
g_order -s md_0_1.tpr -f md_0_1.xtc -n sn2.ndx -d z -od
deuter_sn2.xvg<br>
<br>
<br>
Thank your very much for your support<br>
<br>
Bests</span></div>
<div><br>
</div>
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;">
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;"><font face="Arial" size="2">
<hr size="1"><b><span style="font-weight:bold;">Da:</span></b>
Javier Cerezo <a class="moz-txt-link-rfc2396E" href="mailto:jcb1@um.es"><jcb1@um.es></a><br>
<b><span style="font-weight: bold;">A:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<b><span style="font-weight: bold;">Inviato:</span></b>
Martedì 8 Novembre 2011 9:45<br>
<b><span style="font-weight: bold;">Oggetto:</span></b>
Re: [gmx-users] A question about deuteriu order parameters
graph<br>
</font><br>
Hi Alex<br>
<br>
Deuterium order parameter is a property related to the
relative orientation of molecular axis taking the bilayer
normal as reference. How to use them to extract useful
structural information is a matter of how you interpret the
values regarding their definition (see e.g. Egberts and
Berendsen [J. Chem. Phys.(1988), vol 89, 3718] or Heller et
al [J. Phys. Chem. (1993), vol 97, 8343]). In general, by
comparing order parameters of different systems you can have
some hints about the phase or ordering of your different
systems and how it may change (for example at different
temperature or after insertion of a membrane protein).<br>
<br>
Morover, the usefulness of this paramenter mainly comes from
the fact that they are readily available from simulations
and thus can be used to validate your methodology.
Concretely, experimental information about the deuterium
order parameter (Scd, the one you reported) is spread over
the scientific literature about membranes (see e.g. the
series of papers from the J.F Nagle's group) and it is the
deuterium order parameter commonly reported in MD
simulations. For the case of DPPC you can take for example
the ones from Petrache et al [Biophys. J (2000), vol 79,
3172] and Douliez et al [Biophys. J. (1995), vol 68, 1727].
Take into account that GROMACS g_order tool just numerate
your atoms in the order the order parameters are calculated:
the first Scd comes from the second atom in the index, per
the calculation procedure, so is the CH2 close to the
carbonyl (normally numbered as 2 in the chain).<br>
<br>
In your case, if you compare your graphs with the
experimental ones (pure bilayers), they are significantly
different, which may arise from the fact of the protein
insertion (I doubt it, however) or indicate an incorrect MD
calculation (bad parameters, not well converged...) or
incorrect Scd calculation. Please, post your MD details (FF,
mdp file...) and how you calculated the Scd to continue the
discussion. Did you calculate the Scd on the pure bilayer?<br>
<br>
Javier<br>
<br>
<br>
El 08/11/11 06:41, Alex escribió:<br>
> Dear All,<br>
> <br>
> I run a MD simulation on a membrane protein using DPPC
and I performed a<br>
> deuterium order parameters on the trajectory.<br>
> As I'm a newbie, could you kindly help me to give an
interpretation of these<br>
> graphs?<br>
> <br>
> You can open them at:<br>
> sn1<br>
> <a moz-do-not-send="true"
href="http://www.freeimagehosting.net/137c9"
target="_blank">http://www.freeimagehosting.net/137c9</a><br>
> <br>
> sn2<br>
> <a moz-do-not-send="true"
href="http://www.freeimagehosting.net/6e321"
target="_blank">http://www.freeimagehosting.net/6e321</a><br>
> <br>
> <br>
> Thanks in advance<br>
> <br>
<br>
-- Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tlf.(+34)868887434<br>
<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434</pre>
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