Re: NPAT - NPgT ensemble

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Sun May 03 2009 - 15:54:27 CDT

On Sun, May 3, 2009 at 03:18, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Bjoern,
>
> Bjoern Olausson wrote:
>>
>> Now I got three questions:
>>
>> 1) In my CHARMM setup for NPAT (pmxx 0. pmyy 0. pmzz 2295) pmzz is coupling the
>> box length (z) to the according component of the pressure tensor. Is the keyword
>> "UseConstantArea" working in the same way? As much as I could see, there is
>> no option to couple x or y to the according pressure tensor, so I guess NAMD
>> expects a membrane to be in the X/Y-Plain having the Lipids aligned along the
>> Z-Axis (Actually the standard setup).
>>
>
> This is correct.
>
>> 2) Is my namd config for NPAT/NPgT right?
>>
>
> Looks reasonable to me. I don't speak charmm fluently; you might want to
> consider useConstantRatio if you've got a flag to keep fluctuations in
> the x and y directions isotropic.
>
>> 3) Is it more efficient to use "PMEGridSize{X,Y,Z}" (having the factors 2,3 and
>> 5 in mind) then "PMEGridSpacing"? Is "PMEGridSpacing" automatically calculating
>> the GridSize with respect to the suggested factors?
>>
>
> At least in the current version of the code it looks like the
> automatically calculated sizes follow the small prime factor rule, but
> it will always give you more control to do it by hand.
>
> Best,
> Peter
>

Thanks for your reply Peter,

feels better to have the setup confirmed befor wasting time.

Thanks again.

Kind regards,
Bjoern

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