[gmx-users] problems in numbers of scale down by 0.95 in KALP in DPPC tutorial

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 8/19/14, 5:14 AM, Mahboobe Sadr wrote:
> Dear Dr.lemkul
>
> I used gromacs 453, but i didn't see any difference in these tutorial.
> And also I didn't see a problem like this anywhere to find out more about my
> problem.
>
> May I send you the files and bash history ?
>

No, all you need to do is copy and paste the commands you're giving.

-Justin

> Sent from myMail app for Android
>
> Monday, 18 August 2014, 09:15PM +0430 from Justin Lemkul <jalemkul at vt.edu>:
>
> On 8/18/14, 10:06 AM, Mahboobe Sadr wrote:
>  >
>  > Dear all,
>  > I am new in gromacs and specially in MD simulation of membrane protein,
> in   part "define box and solvent" of justin's tutorial , in scaling down the
> lipids,  I reached an area per lipid of ~69 A^2, after 4 times instead of 26
> times....
>  > I don't know ,where I made a mistake?
>
> Without seeing your exact commands and the corresponding output, there's nothing
> to say.  If you scale each time by 0.95, it is mathematically impossible to
> arrive at a proper APL in this system with only 4 iterations.  At least one of
> your commands or preparation steps was wrong; the outcome is extremely reproducible.
>
> -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
>
> ==================================================
>

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

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

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