[gmx-users] Choosing water molecules and box type and dimensions
Smith, Micholas D.
smithmd at ornl.gov
Fri Apr 29 17:28:12 CEST 2016
As I recall it was the standard TIP3P, so that it could be compared across the force-fields. The biggest difference found in this work between water models was the number of water-protein hydrogen bonds are altered, but peptide-peptide contacts and structure, regardless of water model, were largely influenced by the force-field choice, not the water choice. Now it should be noted that the peptide used was an IDP and has a substantial amount of charged residues for being as small as it is, so your mileage may vary. Also, this work did not test the newest Charmm forcefield so recent notes about the water model choice for that may be different (as you have pointed out).
And I would agree for lipid systems the water model is likely going to matter a whole heck of a lot more. But for aggregation-related IDPs (like the one used in the study) it seems that the force-field choice is really what causes the largest deviations in structural sampling.
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: Friday, April 29, 2016 11:12 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions
On 4/29/16 10:20 AM, Smith, Micholas D. wrote:
> Just to add, a study (http://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00308 ) comparing the 7 force-fields and 3 common water models (for each force-field, except gromos) and found that at least for sampling protein behavior, TIP3P, TIP4P, and SPC/E can all be interchanged between Charmm27, OPLSAA, and Amber force-fields with only minor deviations from one another; i.e. if you compare water models for a given force-field the differences are fairly small.
Was the TIP3P used in the CHARMM simulations the CHARMM-modified TIP3P, or
standard? It makes a difference. It's an even more profound difference in the
case of lipids, but it is important for the proteins nonetheless, as we have
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhijit Kayal <abhijitchemiitd at gmail.com>
> Sent: Friday, April 29, 2016 10:07 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions
> Justin, as always is absolutely right. The paper that I have suggested is
> just compare the different water models with the bulk properties. And the
> bio molecular forcefields are compatible with particular type water
> model. Like charmm force field is compatible with TIP3P water.
> On Fri, Apr 29, 2016 at 6:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 4/29/16 9:51 AM, zeineb SI CHAIB wrote:
>>> Dear all,
>>> Thank your for your answers.
>>> @ Justin,
>>> Where can I found informations related to the compatibility of one water
>>> type with the force field that I choose for my protein? in other words
>>> "where can I found information about the water type that had been used for
>>> the parametrisation of my Force field"?
>> Read the primary literature for the force field you're using. That's of
>> course the first step, otherwise you wouldn't have chosen a force field
>> yet, right? :)
>> Then look for subsequent citations of that force field in application
>> studies related to water. There are a few for each force field, but
>> generally the water model is considered part of the force field and it is
>> rare to deviate from this model. Don't do it unless you have a really,
>> really good reason.
>> 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
>> Gromacs Users mailing list
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> Abhijit kayal
> Research Scholar
> Theoretical Chemistry
> IIT Kanpur
> Gromacs Users mailing list
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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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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