[gmx-users] Re: Peptide folding simulation

Justin Lemkul jalemkul at vt.edu
Wed Jul 18 12:12:10 CEST 2012

On 7/18/12 3:03 AM, jojartb at jgypk.u-szeged.hu wrote:
> Hi,
> Check this article:
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131
> HTH Balazs

In addition, it is important to realize that a single trajectory represents one 
possible outcome, and no matter how long it is, may be stuck in a local energy 
minimum.  In general, multiple simulations of intermediate length are often 
considered better than one long trajectory.  In addition, enhanced sampling 
methods like REMD are used very frequently in studies on protein folding so that 
energy barriers are more easily overcome.


> Quoting simula_460 <bharat.85.monu at gmail.com>:
>> Hi,
>> I tried again simulating the same peptide with OPLS FF for 2000 ns time
>> duration. I used VMD for the secondary structure analysis and trajectory
>> visualization. This time I was able to get folding events but the residues
>> that are should be beta strands were helical for most of the time during
>> simulation. Is it because of the parameters or what else could have gone
>> wrong ??
>> ----
>> --
>> View this message in context:
>> http://gromacs.5086.n6.nabble.com/Peptide-folding-simulation-tp4999215p4999506.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list