SV: SV: [gmx-users] diffusion coefficient with g_msd
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 5 23:54:49 CEST 2009
Sarah Witzke wrote:
> 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?
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-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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>
>
> --
> ----------------------------------
> 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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--
========================================
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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