[gmx-users] area per lipid

[Peter C. Lai]

Not if you aren't going to run those. I assume nvt.mdp and npt.mdp are 
restrained runs to remove/dampen clashes and prevent crashes but if you are
already running a full md simulation then you don't need to redo those steps.

Also, I don't use DispCorr for C36 lipids (some debates about that can be
found on the gromacs mailing list in the past). Setting the constraints to
hbonds and using a TIPS3P water model can also help get POPC APL closer
to experiment, especially if the starting configuration was highly ordered.

On 2012-12-07 10:56:33PM -0800, Shima Arasteh wrote:
> Hi again,
> 
> I edited my md.mdp files. I'm wondering if my nvt.mdp and npt.mdp in charmm36 ff also need such a edition? 
> Also I'd like to know if these mdp file are applicable in any simulation done with charmm36?
> 
> 
> 
> Sincerely,
> Shima
> 
> ________________________________
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
> Sent: Friday, November 9, 2012 3:49 PM
> Subject: Re: [gmx-users] area per lipid
> 
> 
> 
> On 11/9/12 1:46 AM, Shima Arasteh wrote:
> >
> >
> > I pick the snapshots every 10ns, because I don't know how much time this system needs to be simulated to reach to the proper APL.
> >
> 
> What I'm saying is there are far better ways to assess any trends in your data 
> rather than taking 4 snapshots along a much larger trajectory.  You can gather a 
> lot more detail, and very easily.  You're saving snapshots every 2 ps, which 
> means you will have 20000 data points that can be analyzed, rather than just 4.
> 
> > The md.mdp dile I used here is:
> >
> > title        = Production run for Water-POPC system
> >
> > ; Parameters describing the details of the NVT simulation protocol
> > integrator    = md
> > dt        = 0.002
> > nsteps        = 5000000
> >
> > ; Parameters controlling output writing
> > nstxout        = 1000
> > nstvout        = 1000
> > nstenergy    = 1000
> > nstlog        = 1000
> >
> > ; Parameters describing neighbors searching and details about interaction calculations
> > ns_type        = grid
> > nstlist        = 5
> > rlist        = 1.2
> > rcoulomb    = 1.2
> > rvdw        = 1.2
> > pbc        = xyz
> >
> 
> You're using a plain cutoff for the van der Waals interactions, which is 
> incorrect for the CHARMM force fields.  You need the following:
> 
> vdwtype = switch
> rvdw_switch = 0.8
> rvdw = 1.2
> rlistlong = 1.4
> 
> The other settings are fine.
> 
> -Justin
> 
> > ; Parameters for treating bonded interactions
> > continuation    = yes
> > constraint_algorithm = LINCS
> > constraints    = all-bonds
> > lincs_iter    = 1
> > lincs_order    = 4
> >
> > ; Parameters for treating electrostatic interactions
> > coulombtype    = PME
> > pme_order    = 4
> > fourierspacing    = 0.16
> >
> > ; Temperature coupling parameters
> > tcoupl        = Nose-Hoover
> > tc-grps        = POPC SOL
> > tau_t        = 0.5    0.5
> > ref_t        = 300     300
> >
> > ; Pressure coupling parameters
> > pcoupl        = Parrinello-Rahman
> > pcoupltype    = semiisotropic
> > tau_p        = 2.0
> > ref_p        = 1.0    1.0
> > compressibility = 4.5e-5    4.5e-5
> >
> >
> > DispCorr    = EnerPres
> > gen_vel        = no
> > nstcomm        = 1
> > comm_mode    = Linear
> > comm_grps    =POPC SOL
> >
> >
> >
> > Sincerely,
> > Shima
> >
> >
> > ________________________________
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Sent: Friday, November 9, 2012 12:20 AM
> > Subject: Re: [gmx-users] area per lipid
> >
> >
> >
> > On 11/8/12 4:39 AM, Shima Arasteh wrote:
> >> Hi,
> >>
> >> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned in articles ), I let the system to be simulated for 40 seconds. To do so, I checked the area  per lipid every 10 ns. The results of area per lipid in each step are as below:
> >>
> >> 1.
> >> Top leaflet: 60.44
> >>
> >> Bottom leaflet: 59.43
> >>
> >>
> >> 2.
> >> Top leaflet: 61.135
> >> Bottom leaflet: 60.11
> >>
> >> 3.
> >> Top leaflet: 61.40
> >>
> >> Bottom leaflet: 60.38
> >>
> >> 4.
> >> Top leaflet: 60.27
> >>
> >> Bottom leaflet: 59.27
> >>
> >> I expected it to approaches the expected amount steadily, but why did I get such a result? How can I get to the appropriate area  per lipid?
> >>
> >> Would you please give me suggestions? Any suggestions would be appreciated.
> >>
> >
> > Without seeing a complete .mdp file, it's hard to say.  Why are you picking
> > snapshots every 10 ns?  You can easily plot APL over time for the entire
> > trajectory using the box vectors stored in the .edr file from (Box-X *
> > Box-Y)/(number of lipids).  You would have to write your own script to do the
> > calculation, but it's quite straightforward.
> >
> > -Justin
> >
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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