[gmx-users] question

[Justin Lemkul]

On 2/12/14, 6:40 AM, nafas wrote:
> Thank you very much.
> Do you recommend that I do inflate and shrink step for my project??
>

I know nothing about the project.  As I said before, build the system however 
you like based on (1) what makes sense to you, (2) what you can defend to 
reviewers, and (3) what provides an adequate system that can be minimized and 
equilibrated reasonably efficiently.  There are several ways to build such 
systems; I'm not going to tell anyone "this is the way to do it" when I can 
think of probably three or four possible ways.

-Justin

>
>
> On Wednesday, February 12, 2014 2:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/12/14, 3:08 AM, nafas wrote:
>  > Hi Justin.
>  > I hope you have a nice day
>  > I would like to simulate a peptide on the membrane  .In tutorial gromacs that
> simulate peptide
>  > KALP_15 in membrane DPPC ,you use inflate and shrink step.Do I need to do
> this step for my system?
>
> Build the system however you like.  The method I used was simply one that I
> found simple to do, is very reliable, and is easily scripted.
>
>
> -Justin
>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

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

Justin A. Lemkul, Ph.D.
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

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