[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS

[Justin Lemkul]

On 2/26/15 5:39 PM, Thomas Lipscomb wrote:
> Dear gmx-users,
> Ok I understand.  My specific question is how do I do these two tasks:
> 1. What do I need to change about the KALP15 with DPPC tutorial (again substituting maximin 3 for KALP15) so that when I repeat it I get better data, because some parts of the tutorial are just for practice and not for better data, eg. the 1 nanosecond simulation time.

Increased time and probably a better force field.  I strongly recommend CHARMM36.

> 2. What is your general advice about how to simulate several maximin 3 at once interacting with the membrane?  Eg., If I put the maximin 3 somewhat close to each other on or in the membrane at the initial conditions, will they diffuse around enough during the simulation that they can aggregate, or is the diffusion so low that I need to put the maximin 3 in one of the five possible aggregates at the initial conditions of the simulation?  To help you answer this question please see the diagram below that shows the five possible ways that maximin 3 may aggregate.
>

I doubt you'll ever see dynamics on that scale in atomistic simulations 
happening spontaneously.  Consider multiple starting/assembly states and perhaps 
consider coarse graining.

-Justin

> The diagram linked below visualizes all of the five possible ways maximin 3 might be acting to disrupt the membrane and have antimicrobial activity.  The red part of the peptide represents a hydrophilic surface and the blue part represents a hydrophobic surface.  The cylindrical shape of the peptide represents the maximin 3 being an alpha-helix.
>
>
> http://imgur.com/y4yw0Mq
>
> Image was taken from: Tryptophan- and arginine-rich antimicrobial peptides: Structures and mechanisms of action
> Thank you.
> Sincerely,
> Thomas
>
> On 2/24/15 10:18 PM, Thomas Lipscomb wrote:
>> Dear gmx-users,
>> Ok Justin here is the information you asked for:
>>
>
> My questions were rhetorical.  I honestly don't have time to through all of this
> and tell you how to do a thesis project :)
>
> If you have specific questions about using GROMACS to carry out specific tasks,
> that's the main purpose of this list.
>
> -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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