[gmx-users] Semiisotropic pressure coupling

Christopher Neale chris.neale at alum.utoronto.ca
Fri Feb 13 06:33:45 CET 2015

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).

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
> 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
> ; 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 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

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.

More information about the gromacs.org_gmx-users mailing list