On 9/20/16 1:35 AM, Yoo Chan Myung wrote:
Dear Justin,

Thank you for your advice.

I tried to restraint the wandering peptides, because umbrella MD results showed 
'missing z=0.? ‘ errors when I run WHAM analysis.

If I narrow the sampling space from 0.2nm to 0.1nm for umbrella MD simulation, 
could it be a better way to solve the ‘missing z=0.?’ errors than using 
position restraint to keep the wandering peptides in there position according 
to their initial z coordinates?


When reporting errors, always give the full error message, directly copied and pasted from the terminal.

If you're missing regions of the reaction coordinate, then most likely your window spacing was inadequate.

-Justin

Thanks again.

Regards,
Yoochan
On Sep 20, 2016, at 4:32 AM, Justin Lemkul <jalem...@vt.edu> wrote:



On 9/18/16 11:35 PM, Yoo Chan Myung wrote:
Dear gmx users,

I'm trying to simulate membrane penetration with peptide(octamer) using
GROMACS-5.1.2. and I referred the Umbrella Sampling tutorial by Dr. Justin
Lemkul.

After 100 ps umbrella_NPT run, peptides confirmations are still kept in
their initial coordinates. However, after 10ns of umbrella_MD, I cannot get
reliable results for WHAM analysis because the confirmations are quite
deviated from the umbrella_NPT structures.
(plz, refer two results,
https://www.dropbox.com/s/maqwjww8nozmcn6/q_a.jpg?dl=0)

So, my question is should I have to use position restraint for moving
ligands? or just extend simulation time for umbrella_NPT to get equilibrium
structures for umbrella_MD?


What would you restrain?  Don't fall into the trap that many people seem to do 
(despite me warning against it...) and try to follow the tutorial too 
literally.  Restraining the peptide in the tutorial had a specific purpose.  
it's something that probably 99% of umbrella sampling simulations should NOT 
use.

Your structure is basically just falling apart.  You may need some 
inter-peptide restraints to preserve the geometry, but then deconvoluting all 
of that into a meaningful PMF for just pulling the aggregate through the 
membrane becomes very challenging.

-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

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

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

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

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

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