Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Thanks Justin. I will then add manually the constraints on the topology file. Paolo Il giorno gio 7 mag 2020 alle ore 14:56 Justin Lemkul ha scritto: > > > On 5/7/20 8:53 AM, Paolo Costa wrote: > > Dear Justin > > > > that means when I generate the topology file by pdb2gmx I will add > manually > > the section [constraints] on it? > > I suggest you look into the manual to understand different ways of > applying constraints. You can either convert bonds into constraints via > the "constraints" .mdp option, in which case the force constants are > irrelevant but the equilibrium lengths matter, or you do not define any > bonds and manually write in the [constraints]. It depends on how you > need to treat the system. I know nothing about POMs so I can't comment > specifically. If the species is treated as a fully rigid entity (not > something GROMACS is really well suited for), then you should probably > be writing the topology manually because you will have lots of bonds to > non-sequential atoms. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:50 Justin Lemkul ha scritto: > > > On 5/7/20 8:47 AM, Paolo Costa wrote: > > Dear Justin, > > > > I thought too. > > In case, could you please indicate me how I can constrain the interatomic > > distance of a desired molecule, in such case the POM molecule? > > Define [constraints] in the topology for all relevant interatomic > distances. > > -Justin > > > Thanks a lot. > > > > Paolo > > > > Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul > ha > > scritto: > > > >> > >> On 5/7/20 8:41 AM, Paolo Costa wrote: > >>> Dear Justin, > >>> > >>> thanks a lot for your valuable information. > >>> The system (Keggin anion, POM) I am trying to simulate is almost > >> identical > >>> to the one already studied in literature (doi: 10.1021/jp077098p). > >>> In the SI of this work, the authors stated "*Keggin anions are treated > as > >>> rigid particles thus keeping constant the distances between the > different > >>> metal and oxygen atom".* > >>> That means they did not parametrize the bonded interactions for such > >>> molecule, isn't? > >> That sounds to me like all interatomic distances were fixed via > >> constraints, but you should contact the corresponding author to be sure, > >> and ask for example inputs. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> 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. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
On 5/7/20 8:53 AM, Paolo Costa wrote: Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? I suggest you look into the manual to understand different ways of applying constraints. You can either convert bonds into constraints via the "constraints" .mdp option, in which case the force constants are irrelevant but the equilibrium lengths matter, or you do not define any bonds and manually write in the [constraints]. It depends on how you need to treat the system. I know nothing about POMs so I can't comment specifically. If the species is treated as a fully rigid entity (not something GROMACS is really well suited for), then you should probably be writing the topology manually because you will have lots of bonds to non-sequential atoms. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
On 5/7/20 8:47 AM, Paolo Costa wrote: Dear Justin, I thought too. In case, could you please indicate me how I can constrain the interatomic distance of a desired molecule, in such case the POM molecule? Define [constraints] in the topology for all relevant interatomic distances. -Justin Thanks a lot. Paolo Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha scritto: On 5/7/20 8:41 AM, Paolo Costa wrote: Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't? That sounds to me like all interatomic distances were fixed via constraints, but you should contact the corresponding author to be sure, and ask for example inputs. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin, I thought too. In case, could you please indicate me how I can constrain the interatomic distance of a desired molecule, in such case the POM molecule? Thanks a lot. Paolo Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha scritto: > > > On 5/7/20 8:41 AM, Paolo Costa wrote: > > Dear Justin, > > > > thanks a lot for your valuable information. > > The system (Keggin anion, POM) I am trying to simulate is almost > identical > > to the one already studied in literature (doi: 10.1021/jp077098p). > > In the SI of this work, the authors stated "*Keggin anions are treated as > > rigid particles thus keeping constant the distances between the different > > metal and oxygen atom".* > > That means they did not parametrize the bonded interactions for such > > molecule, isn't? > > That sounds to me like all interatomic distances were fixed via > constraints, but you should contact the corresponding author to be sure, > and ask for example inputs. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
On 5/7/20 8:41 AM, Paolo Costa wrote: Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't? That sounds to me like all interatomic distances were fixed via constraints, but you should contact the corresponding author to be sure, and ask for example inputs. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't? Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:20 Justin Lemkul ha scritto: > > > On 5/6/20 11:35 AM, Paolo Costa wrote: > > Dear Gromacs users, > > > > I am interested on studying the interaction between large metal cluster > > anions (polyoxometallates, POM) with different organic cations (e.g > > perylenes, etc..) in water. > > I have already the non bonded parameters of POMs from literature, while > the > > bonded parameters I calculated from Gaussian and VFFDT software. > > If I do not apply a position restraining force on the POM atoms, the POM > > structure gets distorted too much from the experimental one. I guess this > > is due to the lack of a good force field parametrization for > > metal-containing compound. > > *Thus, my question is the following:* > > *can I keep applying a position restraining force on POM atoms during the > > minimization, equilibration and production steps or is it conceptually > > wrong?* > > If you're restraining a configuration because the force field is so bad, > I'd immediately be skeptical of the quality of any simulation. Bonded > parameters are generally easy to reproduce and probably aren't the > source of your problem if you've implemented them carefully, but if > you're trying to combine new bonded parameters with existing nonbonded > parameters, you need to do careful validation on a known system. > > If your system doesn't work, you should back up and make sure you can > reproduce a published study using the same parameters and not ones of > your creation. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
On 5/6/20 11:35 AM, Paolo Costa wrote: Dear Gromacs users, I am interested on studying the interaction between large metal cluster anions (polyoxometallates, POM) with different organic cations (e.g perylenes, etc..) in water. I have already the non bonded parameters of POMs from literature, while the bonded parameters I calculated from Gaussian and VFFDT software. If I do not apply a position restraining force on the POM atoms, the POM structure gets distorted too much from the experimental one. I guess this is due to the lack of a good force field parametrization for metal-containing compound. *Thus, my question is the following:* *can I keep applying a position restraining force on POM atoms during the minimization, equilibration and production steps or is it conceptually wrong?* If you're restraining a configuration because the force field is so bad, I'd immediately be skeptical of the quality of any simulation. Bonded parameters are generally easy to reproduce and probably aren't the source of your problem if you've implemented them carefully, but if you're trying to combine new bonded parameters with existing nonbonded parameters, you need to do careful validation on a known system. If your system doesn't work, you should back up and make sure you can reproduce a published study using the same parameters and not ones of your creation. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
