[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Justin Lemkul]

On 10/3/14 6:21 AM, Anurag Dobhal wrote:
> hello Justin thanks for your reply.
>
> I am unable to understand how to proceed in this tutorial. I am working on
> it from many days but I am unable to do.
>
> I have understood till the step.
>
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>
> this is the result which I got.
>
> Area per protein: 2 nm^2
> Area per lipid: 10.4716089904762 nm^2
>
> Area per protein, upper half: 1.75 nm^2
> Area per lipid, upper leaflet : 10.4755772444444 nm^2
>
> Area per protein, lower half: 2 nm^2
> Area per lipid, lower leaflet : 10.4716089904762 nm^2
>
> Writing Area per lipid...
> Done!
>
>
> and the minimization step after that. I get the confout.gro file.
>
>
> I am confused how to continue from the step
>
> "perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
> area_shrink1.dat"
>
> how many times do we need to run this command, nd with what changes ????
>

Think about what you're doing.  The first inflation step spread the lipids out, 
deleted ones that still contacted the protein, and then you ran minimization. 
So it's a totally nonphysical, but useful, step.  Then you scaled the lipids 
back towards the protein by a factor of 0.95, creating yet another nonphysical 
system that is a step closer to being useful.  Visualize it.  Does it make sense 
to solvate?  Of course not; you have a huge amount of void space and the bilayer 
is not physically sensible.  The APL is over 100 A^2, and the target is 
somewhere in the ballpark of 62 A^2.  So clearly you need to keep going.  So you 
minimize system_shrink1.gro as you did before; note the topology is at this 
point constant as you are no longer deleting lipids.

So you need to keep going.  What makes sense as input and output?  Well, as the 
tutorial says:

"After 26 iterations of scaling down by 0.95, I reached an area per lipid of ~71 
A^2, above the experimental value of ~62 A^2. Since the script tends to 
overestimate the area per lipid, this value is good enough to continue to 
equilibration."

So your new input is the energy-minimized system_shrink1.gro (verbose file 
naming here is a good idea rather than calling everything "confout.gro," because 
that is terribly confusing), and you use InflateGRO to scale down again to 
obtain system_shrink2.gro.  Note the APL will still be inadequate.  Minimize, 
shrink, check, minimize, shrink, check... This is why I say it is very easy to 
script this process in a loop.

> and how to solvate the system  ( which file ) and what will be the command ???
>

Surely you can determine how to do this after consulting some basic tutorial 
material.  Aside from the minor modification of vdwradii.dat (described in 
detail in the tutorial), genbox (gmx solvate) pretty much always works the same 
way.  If this is unfamiliar, repeat more basic tutorials and/or read the manual 
until you are clear on what to do.  There is a reason the membrane tutorial is 
considered more advanced; to better teach users to think critically about what 
they are doing, I specifically do not list every single step, lest the user 
simply assume the "correct" procedure for doing such things is simply "type 
this, now type this, now type this..."  I think that's a disservice to those 
trying to learn.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================