[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Dear Justin,

Thanks for the continuous help.

Since I have done reverse CG, The CG POPC was equilibrated alone
anisotropically, The APL was fine there.
On reverse CG and NVT its still fine, it only after NPT it starts dropping.

I am calculating APL as (2*Lx*Ly)/(No. of Lipids).

You mentioned to get gull force field from your site, is it here:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

On unzipping this I see POPC is an .trp entry.

If there is some other database, kindly point it out to me.

Thanks,

sxn


On Sun, Feb 15, 2015 at 11:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/15/15 11:40 AM, Justin Lemkul wrote:
>
>>
>>
>> On 2/15/15 11:32 AM, shivangi nangia wrote:
>>
>>> Sorry about that.
>>>
>>> Here it is:
>>> https://drive.google.com/file/d/0B9SJqGLyLrwVcThWbEthaFo3SGc/
>>> view?usp=sharing
>>>
>>>
>> So this is actually a system in which a peptide is peripherally bound to
>> a POPC
>> membrane.  That complicates things significantly.  Not only is it less
>> straightforward to calculate APL, but you have to consider that the
>> protein
>> itself perturbs the lipid properties.  If you want to evaluate the
>> validity of
>> the parameters, you need to be running a simulation of a pure POPC
>> membrane.
>>
>> How have you calculated APL?  Have you run a pure POPC membrane
>> simulation?
>> These are the only things worth spending time on.  Otherwise, all you're
>> seeing
>> is either (1) a problem with how you're calculating APL and/or (2)
>> effects of
>> the peptide.
>>
>>
> Also, it looks like the "CHARMM36" files you are using come from the
> GROMACS download site, which come from Tom's work.  He has since clarified
> that those force field files are CHARMM36 lipids only, therefore the
> protein parameters are CHARMM22/CMAP, thus not the self-consistent CHARMM36
> force field that our lab produces.  You could be getting artifacts there,
> as well, though I can't specifically say offhand what those might be.  But
> the files from the GROMACS site should be used ONLY for pure lipid
> simulation.  For anything else, get the full force field from our site.
>
> -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
>
> ==================================================
>