[gmx-users] Semiisotropic pressure coupling
t.piggot at soton.ac.uk
Fri Feb 13 17:58:13 CET 2015
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
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).
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.
>> Thank you,
>> 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
>>> 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
>> tensor is used to calculate pressures in the x-y and z dimensions
>> 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
>> 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
>> 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 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
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Dr Thomas Piggot
University of Southampton, UK.
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