[gmx-users] Semiisotropic pressure coupling

Fri Feb 13 22:00:35 CET 2015

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
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>

--
Dr Thomas Piggot
University of Southampton, UK.

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.