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?
> 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
>> 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,
>> 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
> 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 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
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