Re: [gmx-users] Grompp error for graphene modeling
Thanks Justin for your help. I will modify the force field again to model the particles better. Best,Mohammad From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Saturday, 27 May 2017, 23:20:26 Subject: Re: [gmx-users] Grompp error for graphene modeling On 5/27/17 3:33 AM, Mohammad Roostaie wrote: > Hi All, > I modeled graphene in a box of water with a peptide in the center of the box. > I modified the OPLS-AA force field by adding the parameters from this link to > the modified force field: http://chembytes.wikidot.com/grocnt. But, when I > want to add ions to the system, I got this warning: > WARNING 1 [file ffbonded.itp, line 305]: Overriding Bond parameters. > old: 0.151 292880 0.151 292880 >new: C C 1 0.14000 392459.2 > Actually, in the ffbonded.itp file, I put two parameters for C-C which the > new one referes to the graphene, and, I cannot change the names in the itp > file since the graphene atom names are C.Is this an important warning (May it > affect the stability of the system and results)? Or may I use -maxwarn? Atom *names* and *types* are different beasts. Types are used in ffnonbonded.itp and applied to the atoms found in the topology. Atom names are irrelevant for parameter assignment. But here you have introduced clearly conflicting parameters that will alter the behavior of the conflicting types, e.g. any aromatic rings in your peptide will behave incorrectly if you proceed with what you're doing. In general, do not use -maxwarn unless you can clearly articulate why you're overriding a serious warning from grompp, not simply to make a problem go away. -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. -- 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] Grompp error for graphene modeling
On 5/27/17 3:33 AM, Mohammad Roostaie wrote: Hi All, I modeled graphene in a box of water with a peptide in the center of the box. I modified the OPLS-AA force field by adding the parameters from this link to the modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to add ions to the system, I got this warning: WARNING 1 [file ffbonded.itp, line 305]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 10.14000 392459.2 Actually, in the ffbonded.itp file, I put two parameters for C-C which the new one referes to the graphene, and, I cannot change the names in the itp file since the graphene atom names are C.Is this an important warning (May it affect the stability of the system and results)? Or may I use -maxwarn? Atom *names* and *types* are different beasts. Types are used in ffnonbonded.itp and applied to the atoms found in the topology. Atom names are irrelevant for parameter assignment. But here you have introduced clearly conflicting parameters that will alter the behavior of the conflicting types, e.g. any aromatic rings in your peptide will behave incorrectly if you proceed with what you're doing. In general, do not use -maxwarn unless you can clearly articulate why you're overriding a serious warning from grompp, not simply to make a problem go away. -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.
[gmx-users] Grompp error for graphene modeling
Hi All, I modeled graphene in a box of water with a peptide in the center of the box. I modified the OPLS-AA force field by adding the parameters from this link to the modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to add ions to the system, I got this warning: WARNING 1 [file ffbonded.itp, line 305]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14000 392459.2 Actually, in the ffbonded.itp file, I put two parameters for C-C which the new one referes to the graphene, and, I cannot change the names in the itp file since the graphene atom names are C.Is this an important warning (May it affect the stability of the system and results)? Or may I use -maxwarn? Best,Mohammad -- 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.
