[gmx-users] Semiisotropic pressure coupling
shivangi.nangia at gmail.com
Fri Feb 13 04:30:07 CET 2015
Thanks for the reply.
The link you have mentioned says the parameters are for GROMACS 5.0
I am using an older version, 4.6.1
Is there another link/suggestions for that version.
Thanks so much,
> 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
>> 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 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 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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