[gmx-users] Semiisotropic pressure coupling

Justin Lemkul jalemkul at vt.edu
Fri Feb 13 02:41:31 CET 2015

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


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