@Justin, 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. -Micholas ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Friday, April 29, 2016 11:12 AM To: gmx-us...@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 recently discovered. -Justin > -Micholas > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of abhijit > Kayal <abhijitchemi...@gmail.com> > Sent: Friday, April 29, 2016 10:07 AM > To: gmx-us...@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 <jalem...@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 >> >> -- >> ================================================== >> >> 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 >> 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-requ...@gromacs.org. >> > > > > -- > Abhijit kayal > Research Scholar > Theoretical Chemistry > IIT Kanpur > -- > 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-requ...@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 jalem...@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-requ...@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-requ...@gromacs.org.
