[gmx-users] Question Re. KALP-15 in DPPC tutorial

Justin Lemkul jalemkul at vt.edu
Sat Jan 25 20:34:55 CET 2014

On 1/25/14, 8:15 AM, jhosamelly wrote:
> I got into this part of the KALP-15 in DPPC tutorial
> "Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"):
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> Follow this up by another round of EM. During the "shrinking" steps, be sure to change the cutoff value to 0, or else you will continue to delete lipids! After 26 iterations of scaling down by 0.95, I reached an area per lipid of ~71 Å2, above the experimental value of ~62 Å2. Since the script tends to overestimate the area per lipid, this value is good enough to continue to equilibration."
> I added the line at the topol.top [molecule]
> DDPC     126

That can't be right; the lipid is named DPPC.  Though inconsequential in this 
case (I am assuming it is a typo), the larger point here is if you are not 
copying and pasting everything you are posting, it is error-prone, which slows 
down the speed with which you will receive a result.

> Then I tried
> grompp -f minim.mdp -c system_inflate.gro -p topol.top -o em.tpr -maxwarn 1
> Somehow, it worked. But I didn't get any confout.gro file so the

grompp doesn't produce confout.gro.  The job of grompp is to produce a .tpr 
file, which is then run by mdrun, which does produce confout.gro (the default 
file name for -c, the final configuration of the run).

> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat

Likely because you didn't execute mdrun after grompp.  Refer to more basic 
tutorial material for common workflows.  The membrane tutorial does not tell you 
every single step explicitly; some prior knowledge is expected.

You can send tutorial questions directly to me rather than spamming the list 
with questions about every step.



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


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