SV: SV: [gmx-users] diffusion coefficient with g_msd

Sarah Witzke sawit02 at student.sdu.dk
Fri Jun 5 23:43:58 CEST 2009


Fra: gmx-users-bounces at 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?
> 
>
> 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-bounces at 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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>>    
>
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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.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole <http://md.chem.rug.nl/~periole> 
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