[gmx-users] Semiisotropic pressure coupling
Justin Lemkul
jalemkul at vt.edu
Sun Feb 15 17:41:33 CET 2015
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.
-Justin
>
> Shivangi Nangia, Ph. D
> Postdoctoral Research Associate
> Department of Molecular and Cell Biology
> University of Connecticut
>
> On Sun, Feb 15, 2015 at 11:13 AM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 2/15/15 10:53 AM, shivangi nangia wrote:
>
> Hello Justin,
>
> Please find the files in the link below:
> https://drive.google.com/__folderview?id=__0B9SJqGLyLrwVa3MxME1IYjZJS0k&__usp=sharing
> <https://drive.google.com/folderview?id=0B9SJqGLyLrwVa3MxME1IYjZJS0k&usp=sharing>
>
>
> It also contains a readme file.
>
> Thanks so much for all your help.
>
> Please let me know if you need anything else.
>
>
> Please upload a tarball with all the files so I don't have to download
> dozens of things individually.
>
> -Justin
>
> Thanks a lot,
>
>
>
> Shivangi Nangia, Ph. D
> Postdoctoral Research Associate
> Department of Molecular and Cell Biology
> University of Connecticut
>
> On Sun, Feb 15, 2015 at 7:59 AM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> On 2/14/15 9:52 PM, shivangi nangia wrote:
>
> Hello Justin,
>
> I ran the simulation for 100 ns and I still get low APL at 303
> K, 0.58 nm^2
> :(
>
>
> That outcome is inconsistent with everything I have seen from our own
> internal testing and published works that use GROMACS. Something
> else must
> be up. If you post all of your input files somewhere that I can
> download
> them, I'll try to take a look.
>
> -Justin
>
>
> Thanks in advance.
> sxn
>
>
>
>
>
> On Fri, Feb 13, 2015 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> On 2/13/15 5:00 PM, shivangi nangia wrote:
>
> Hello All,
>
> Thank you all for you input.
>
> I now have access to GROMACS 5.0.
>
> On using the recommended settings, the APL is sill dropping
> within 3 ns of
> the simulation.
>
>
> 3 ns is orders of magnitude too short to draw any
> conclusions. Simulate
> out to 100 ns and we'll talk :) I only say this because I
> know the
> APL can
> be reproduced with the settings I gave in CHARMM and
> GROMACS with very
> close agreement.
>
> <snip>
>
> nstlist = 1
>
>
>
> Yikes! You're losing a ton of performance here (though
> check the log to
> make sure Verlet adjusted this to something more
> suitable). Setting
> nstlist = 1 is only for energy minimization.
>
>
> -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
> <mailto:jalemkul at outerbanks.__umaryland.edu
> <mailto:jalemkul at outerbanks.umaryland.edu>> | (410) 706-7441
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> --
> ==============================____====================
>
> 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
> <mailto:jalemkul at outerbanks.__umaryland.edu
> <mailto:jalemkul at outerbanks.umaryland.edu>> | (410) 706-7441
> <tel:%28410%29%20706-7441>
> <tel:%28410%29%20706-7441>
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> --
> ==============================__====================
>
> 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
> <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> <tel:%28410%29%20706-7441>
> http://mackerell.umaryland.__edu/~jalemkul
> <http://mackerell.umaryland.edu/~jalemkul>
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> ==============================__====================
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>
--
==================================================
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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