[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

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
>
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-- 
==================================================

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

==================================================