Re: [gmx-users] Entering ions
On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote: Dear users I want to use some ions in my simulation (Phosphorus, Sulfur and ...). How can I know in which FF these are present? Phosphorus and sulfur aren't ions. There are P and S atomtypes in most force fields that are suitable for several types of functional groups, but I suspect your description simply isn't accurate enough to begin to guess. And what can I do if no FF include the interested Ions? The answer to this question is always the same - derive them in a manner consistent with a force field you have reason to believe will be adequate for simulating the species of interest. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Entering ions
Dear Dr. Justin Thank you for your reply You are right, I am sorry for my mistake. I meant Phosphate and Sulfate ions. I want to have these ions in my solution. On Mon, Oct 21, 2013 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote: Dear users I want to use some ions in my simulation (Phosphorus, Sulfur and ...). How can I know in which FF these are present? Phosphorus and sulfur aren't ions. There are P and S atomtypes in most force fields that are suitable for several types of functional groups, but I suspect your description simply isn't accurate enough to begin to guess. And what can I do if no FF include the interested Ions? The answer to this question is always the same - derive them in a manner consistent with a force field you have reason to believe will be adequate for simulating the species of interest. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Entering ions
On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote: Dear Dr. Justin Thank you for your reply You are right, I am sorry for my mistake. I meant Phosphate and Sulfate ions. I want to have these ions in my solution. Many force fields include these ions or closely related model compounds. Have a look in the .rtp entries and search the literature. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Entering ions
sure, thank you. On Mon, Oct 21, 2013 at 4:49 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote: Dear Dr. Justin Thank you for your reply You are right, I am sorry for my mistake. I meant Phosphate and Sulfate ions. I want to have these ions in my solution. Many force fields include these ions or closely related model compounds. Have a look in the .rtp entries and search the literature. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
