[gmx-users] Semiisotropic pressure coupling
shivangi nangia
shivangi.nangia at gmail.com
Fri Feb 13 23:00:33 CET 2015
Hello All,
Thank you all for you input.
I now have access to GROMACS 5.0.
On using the recommended settings, the APL is sill dropping within 3 ns of
the simulation.
This means as suggested in this discussing that the cut off parameters are
playing a crucial role.
Also, time-step as mentioned in the paper link.
My mdp for GROMACS 5.0 is:
Are there any parameters you suggest should be modified/explored?
; RUN CONTROL PARAMETERS
dt = 0.002
;nsTEPS = 12500000 ;25ns
nsTEPS = 25000000 ;50ns
integrator = md
ld-seed = -1
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 50000
nstvout = 50000
energygrps = Protein Non-Protein
; Output frequency for energies to log file and energy file
nstlog = 100
nstcalcenergy = -1
nstenergy = 100
nstxtcout = 500
xtc-precision = 1000
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 1
rlist
; ns algorithm (simple or grid)
ns-type = Grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
;rcoulomb-switch = 0
rcoulomb = 1.2
fourierspacing = 0.16
pme_order = 4
optimize-fft = yes
; Method for doing Van der Waals
vdw-type = cutoff
; cut-off lengths
rvdw-switch = 1.0
rvdw = 1.2
cutoff-scheme = Verlet
vdw-modifier = force-switch
;vdw-modifier = Potential-Shift
DispCorr = no
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = Lincs
lincs-order = 6
; temperature controls
tcoupl = v-rescale
tc-grps = Protein Non-Protein
tau-t = 1.0 1.0
ref-t = 303 303
; Pressure Controls
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau-p = 1.0
ref-p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut
On Fri, Feb 13, 2015 at 4:00 PM, Piggot T. <T.Piggot at soton.ac.uk> wrote:
> Hi,
>
> In addition to my previous message, I thought i would also add in my 2
> pennies (cents) worth to the discussion on lipid force fields and cut-off's:
>
> From the fairly large range of force fields and simulation parameters I
> have looked at with simple PC membranes, Chris you are most definitely
> correct that changing the van der Waals cut-off can have a large impact
> upon the membrane properties (e.g. see the results for the Berger
> parameters in the paper I linked to previously and in particular properties
> like the lipid diffusion). Despite this, I would also say that the CHARMM36
> force field was bar far the most sensitive to small changes in the LJ
> cut-off. For me this is of concern and an area I would imagine there is
> work currently underway (Justin could probably tell us more in this
> regard). Despite these concerns, if you do use the appropriate cut-off's,
> etc. with this force field I would say that it is generally the most
> accurate in terms of reproducing the details of the lipid membrane (e.g.
> deuterium order parameters, membrane thickness, etc.). Given the fact that
> C36 lipids have faster diffusion than many of the united
> -atom force fields out there and this therefore will offset some of the
> computational costs associated with using this force field, I would most
> likely recommend this if someone asked me which force field they should use
> for a PC lipid membrane. Obviously adding in other components, etc. and
> things get even more complicated but a CHARMM force field still probably
> remains a good choice.
>
> Cheers
>
> Tom
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Thomas
> Piggot [t.piggot at soton.ac.uk]
> Sent: 13 February 2015 16:50
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Semiisotropic pressure coupling
>
> Hi Chris/Justin,
>
> I observed this impact upon membrane area dramatically with DPPC when
> testing both the water model (TIP3P and CHARMM TIP3P) and the switching
> mechanism (potential and force). See the table 3 in the SI of the
> following paper:
>
> http://pubs.acs.org/doi/abs/10.1021/ct3003157
>
> At the time, the version of GROMACS didn't have force switching and so I
> used NAMD for these simulations (as I suspected the gel phase seen with
> DPPC in GROMACS was a combination of both normal TIP3P and the switching
> off of the potential rather than force).
>
> Cheers
>
> Tom
>
> On 13/02/15 14:37, Justin Lemkul wrote:
> >
> >
> > On 2/13/15 12:18 AM, Christopher Neale wrote:
> >> Dear Justin:
> >>
> >> If you have time, can you please provide a link / reference for your
> >> comment that potential switching leads to errors in the charmm lipid
> >> force field? I tried a google search, but couldn't come up with
> >> anything specific. You mentioned noticeable artifacts, so I'm hoping
> >> that you can point me at these (or is it just that changing anything
> >> about the LJ cutoffs changes the APL, which is pretty general across
> >> all lipid force fields in my experience).
> >>
> >
> > No reference or link; this is just an issue that gets reported to the
> > CHARMM community/developers frequently. I have a bunch of emails
> > related to this particular issue, but you can't really cite those :)
> > With the increase in activity on the Membrane Builder of CHARMM-GUI,
> > it seemed that people were running into issue due to
> > misinterpretations of literature (though it is clearly stated that
> > forces are switched in the parametrization). With our introduction of
> > GROMACS 5.0-compatible inputs, the reports of problems have
> > diminished. Everyone reported the same thing - dramatic decrease (10%
> > or more) in APL. You're correct that this is not unique to CHARMM
> > lipids, it just seemed like a frequent problem for us because a lot of
> > users thought "vdwtype = switch" was correct. Common misconception,
> > that even I screwed up in the past.
> >
> > -Justin
> >
> >> Thank you,
> >> Chris.
> >>
> >> ________________________________________
> >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> >> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> >> Justin Lemkul <jalemkul at vt.edu>
> >> Sent: 12 February 2015 20:41
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Semiisotropic pressure coupling
> >>
> >> On 2/12/15 8:15 PM, shivangi nangia wrote:
> >>> Hello All,
> >>>
> >>> I am doing all-atom simulation with charmm 36 ff (obtained from
> >>> reverse CG
> >>> using the script provided by Tsjerk)
> >>> The system consists of popc, 21 AA protein, water and ions.
> >>>
> >>> After reverse CG I did short EM and 5 ns NVT simulation.
> >>> However, when I do NPT simulation, the area per lipid drops from 67
> >>> ang2 to
> >>> 57 within 1 ns ( x and y dimensions decrese and z increases).
> >>>
> >>> I am using semiisotropic pressure coupling.
> >>>
> >>> I have a question regarding that.
> >>> I noticed in example .mdps and the tutorial by Justin Lemkul
> >>>
> >>>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/npt.mdp
> >>>
> >>>
> >>>
> >>>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/md.mdp
> >>>
> >>>
> >>>
> >>> tau_p is specified, the ref_p and compresibility is same, does not that
> >>> mean essentially I am doing isotropic coupling?
> >>>
> >>
> >> No, that does not indicate isotropic pressure coupling. The full
> >> pressure
> >> tensor is used to calculate pressures in the x-y and z dimensions
> >> separately.
> >> The values of tau_p and compressibility are simply used for
> >> calculating the
> >> response time of the barostat.
> >>
> >> The problem is that your nonbonded settings are incorrect:
> >>
> >>> ; nblist cut-off
> >>> rlist = 1.2
> >>>
> >>> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >>> ; Method for doing electrostatics
> >>> coulombtype = PME
> >>> rcoulomb-switch = 0
> >>> rcoulomb = 1.2
> >>> fourierspacing = 0.16
> >>> pme_order = 4
> >>> optimize-fft = yes
> >>> ; Method for doing Van der Waals
> >>> vdw-type = switch
> >>> ; cut-off lengths
> >>> rvdw-switch = 1.0
> >>> rvdw = 1.2
> >>>
> >>
> >> Note that potential switching leads to errors in the lipid force
> >> field. You
> >> need a buffered neighbor list with force switching. The exact
> >> parameters that
> >> you should use are listed on
> >> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM.
> >> For
> >> lipids, you should absolutely not deviate from these settings. The
> >> protein and
> >> nucleic acid force fields (and the remainder of CHARMM additive
> >> models) should
> >> use these settings, though they are more forgiving (i.e. potential
> >> switching
> >> does not lead to noticeable artifacts). With lipids, the
> >> requirements are
> >> pretty absolute. People frequently report a drop in APL; every time
> >> they do,
> >> it's because they're using the wrong settings.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
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> >
>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
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