[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Dear Justin,
>

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,

Best,
sxn

>
>
> 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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