[gmx-users] Force-field bias???

[SAPNA BORAH]

Thank you Justin, Vitaly.
Thank you @Micholas, the paper you referred is helping me clear many of my
queries. I will continue to look for answers keeping your valuable comments
in mind.

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Wed, Aug 5, 2015 at 10:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/5/15 10:32 AM, Smith, Micholas D. wrote:
>
>> OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in
>> folding
>> (in both my experience, and from   doi:10.1016/j.bpj.2009.04.061 ). That
>> is
>> not necessarily a bad thing if the peptide is suppose to take a while to
>> fold. If you just want to get to the folded structure, and you don't care
>> about the pathway, you could also use an enhanced sampling technique.
>>
>> An alternative force-field that seems to handle beta structures pretty
>> well,
>> but can sometime accelerate the folding is the older GROMOS53A
>> force-field;
>> though since it is united atom, I have found that sometime the contacts
>> don't
>> quite match with NMR data.
>>
>>
> Beware, it's well known that 53A6 systematically under-stabilizes helices
> such that you get inappropriate unfolding.  It samples the unfolded state
> quite well, but again, this may be application-specific.
>
> -Justin
>
>
> Force-field choice is a non-trival, but largely difficult problem to deal
>> with. In general, though, I tend to avoid the older Amber force-fields
>> when
>> simulating beta-rich peptides as have had a bias towards helical
>> structures
>> (see the references within the paper I noted above).
>>
>> Good Luck,
>>
>> Micholas
>>
>> =================== Micholas Dean Smith, PhD. Post-doctoral Research
>> Associate University of Tennessee/Oak Ridge National Laboratory Center for
>> Molecular Biophysics
>>
>> ________________________________________ From:
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of SAPNA
>> BORAH
>> <sapnauser365 at gmail.com> Sent: Wednesday, August 05, 2015 10:20 AM To:
>> gmx-users at gromacs.org Subject: Re: [gmx-users] Force-field bias???
>>
>> Dear all,
>>
>> Thank you for your answers which definitely clears some of my doubts. I am
>> trying to unfold a lectin tetramer protein that comprises largely of beta
>> strands, and I have used the OPLS ff, so far I have not been successful,
>> can
>> OPLS be a problem at all??
>>
>> Thanks..
>>
>> Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University,
>> India
>>
>> On Wed, Aug 5, 2015 at 5:44 PM, Smith, Micholas D. <smithmd at ornl.gov>
>> wrote:
>>
>> You should also note that force-field bias may be system dependent. So if
>>> you are unsure of the dynamics from the onset, you should likely test a
>>> variety of force-fields and/or try to find a comparison to NMR (or other)
>>> experimental methods.
>>>
>>> -Micholas
>>>
>>> =================== Micholas Dean Smith, PhD. Post-doctoral Research
>>> Associate University of Tennessee/Oak Ridge National Laboratory Center
>>> for
>>> Molecular Biophysics
>>>
>>> ________________________________________ From:
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
>>> Lemkul <jalemkul at vt.edu> Sent: Wednesday, August 05, 2015 7:31 AM To:
>>> gmx-users at gromacs.org Subject: Re: [gmx-users] Force-field bias???
>>>
>>> On 8/5/15 6:24 AM, SAPNA BORAH wrote:
>>>
>>>> Dear all,
>>>>
>>>> I have a general query about unfolding simulations. Is there a bias
>>>> among force-fields selected for unfolding, i.e. is it possible that
>>>> unfolding
>>>>
>>> of
>>>
>>>> the protein may be different with a change in force fields applied?
>>>> Literature has given some support on this, however, I am not sure how
>>>>
>>> this
>>>
>>>> may happen.
>>>>
>>>>
>>> Yes, this is true.  It usually comes down to errors in the balance
>>> between
>>> intra-protein and protein-water interactions.  Incorrect balance favors
>>> either the folded or unfolded state.  No force field is perfect, but some
>>> are better than others and there's lots of literature on this topic
>>> regarding which are the most successful.
>>>
>>> -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
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ================================================== -- Gromacs Users
>>> mailing
>>> list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send
>>> a mail to gmx-users-request at gromacs.org.
>>>
>>> -- Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send
>>> a mail to gmx-users-request at gromacs.org.
>>>
>>> -- Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a
>> mail to gmx-users-request at gromacs.org.
>>
>>
> --
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>