Re: [gmx-users] spc.itp file and flexspc.itp
On 6/5/18 8:48 AM, Anjana Jayasinghe wrote: Dear Prof. Justin and Gromacs users, Thank you very much for the reply. I noticed that FLEX_SPC is defined in the .top file of the bilayer simulations for CiEj systems ( in patrickfuchs/CiEj_2016H66 ). They used a modified force field known as 2016H66 with Gromacs 4.0.7. I am also trying to use it for my CiEj system with Gromacs 2016 version. Since they have achieved the lamellar region by defining the FLEX_SPC, do I have to use the same FLEX_SPC in my .top? Could you please comment on this. When reproducing previous work, yes, you should do exactly as the authors did. However, GROMACS 4.0.7 is wildly outdated and that's why you should note that "flexspc.itp" no longer exists, but you can in fact use a flexible SPC model by using the standard "spc.itp" with "define = -DFLEXIBLE." They are functionally identical. -Justin Thank you. | | | | | | | | | | | patrickfuchs/CiEj_2016H66 CiEj_2016H66 - This repositery contains files to simulate CiEj surfactants using the GROMOS-compatible 2016H66 f... | | | On Monday, 4 June 2018, 10:05:12 pm AEST, Justin Lemkul wrote: On 6/4/18 6:13 AM, Anjana Jayasinghe wrote: Dear Gromacs Users, Is there any difference in the simulation, if we define the spc.itp as, | #ifdef FLEX_SPC | | | #include "flexspc.itp" | | | #else | | | #include "spc.itp" | | | #endif | instead of using the single line #include "spc.itp" ? Can anyone help me to understand the difference? Have you looked at the contents of flexspc.itp? You'll note that it has no functional content as this was an old way of defining flexible water. Don't do what you have shown above. If you want flexible water, use "define = -DFLEXIBLE" and the normal spc.itp in your topology. Again, inspect that file's contents to understand what it is doing. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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] spc.itp file and flexspc.itp
Dear Prof. Justin and Gromacs users, Thank you very much for the reply. I noticed that FLEX_SPC is defined in the .top file of the bilayer simulations for CiEj systems ( in patrickfuchs/CiEj_2016H66 ). They used a modified force field known as 2016H66 with Gromacs 4.0.7. I am also trying to use it for my CiEj system with Gromacs 2016 version. Since they have achieved the lamellar region by defining the FLEX_SPC, do I have to use the same FLEX_SPC in my .top? Could you please comment on this. Thank you. | | | | | | | | | | | patrickfuchs/CiEj_2016H66 CiEj_2016H66 - This repositery contains files to simulate CiEj surfactants using the GROMOS-compatible 2016H66 f... | | | On Monday, 4 June 2018, 10:05:12 pm AEST, Justin Lemkul wrote: On 6/4/18 6:13 AM, Anjana Jayasinghe wrote: > Dear Gromacs Users, > Is there any difference in the simulation, if we define the spc.itp as, > > | #ifdef FLEX_SPC | > | | #include "flexspc.itp" | > | | #else | > | | #include "spc.itp" | > | | #endif | > > > instead of using the single line #include "spc.itp" ? > Can anyone help me to understand the difference? Have you looked at the contents of flexspc.itp? You'll note that it has no functional content as this was an old way of defining flexible water. Don't do what you have shown above. If you want flexible water, use "define = -DFLEXIBLE" and the normal spc.itp in your topology. Again, inspect that file's contents to understand what it is doing. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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. -- 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] spc.itp file and flexspc.itp
On 6/4/18 6:13 AM, Anjana Jayasinghe wrote: Dear Gromacs Users, Is there any difference in the simulation, if we define the spc.itp as, | #ifdef FLEX_SPC | | | #include "flexspc.itp" | | | #else | | | #include "spc.itp" | | | #endif | instead of using the single line #include "spc.itp" ? Can anyone help me to understand the difference? Have you looked at the contents of flexspc.itp? You'll note that it has no functional content as this was an old way of defining flexible water. Don't do what you have shown above. If you want flexible water, use "define = -DFLEXIBLE" and the normal spc.itp in your topology. Again, inspect that file's contents to understand what it is doing. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
[gmx-users] spc.itp file and flexspc.itp
Dear Gromacs Users, Is there any difference in the simulation, if we define the spc.itp as, | #ifdef FLEX_SPC | | | #include "flexspc.itp" | | | #else | | | #include "spc.itp" | | | #endif | instead of using the single line #include "spc.itp" ? Can anyone help me to understand the difference? Thank you. -- 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.
