[gmx-users] Energy minimization has stopped

[Anurag Dobhal]

Thanks a lot Justinn and Mark for the valuable suggestions.

I will start over again by choosing a force field which is suitable for the
RNA molecules.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/23/16 7:17 AM, Anurag Dobhal wrote:
>
>> Dear Justin,
>>
>> The main aim of the study is to study the interaction between a polymer
>> (chitosan) and RNA molecules by simulating them togather. I have already
>> successfully simulated my polymer system using OPLS AA force field.
>>
>> To simulate them together I need to write the OPLS AA parameters for RNA
>> molecules. I was suggested (Link Below) earlier that I can take the
>> charges
>> from any other forcefield.
>>
>> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
>>
>> please enlight me where I am going wrong.
>>
>>
> I think you misunderstood what I said in that thread.
>
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html
>
> "You should find force field parameters specifically for the base from
> published literature or from another force field."
>
> This means: find a force field that has parametrized the species you need
> and use it.  This does not mean: hack together something from "any other
> force field" you like and try to make it OPLS-AA.  You did not say before
> that you were dealing with a complex system like this.  You just said your
> guanine charges didn't add up.  So I addressed that problem.
>
> Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an
> invalid approach.
>
> Pick a force field.  Use that force field.  Do not try to kludge together
> some hybrid entity.  Force fields are designed to be internally
> self-consistent.  If you do not have a proper balance of interactions, you
> are not doing a useful simulation.  You are generating random numbers.
>
>
> -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
>
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