Re: [gmx-users] Qm/mm
Hi Albert, I want to study the interaction of functionalized inorganic nanotube with protein. I just can use free software. Is ORCA ok for my needs? I don't know anything about it.i couldn't use some softwares like Gaussian and quantum espresso because Gaussian is commercial and Quantum Espresso is not Ok for nanotube with more than 100 atoms... Is ORCA suitable for these systems?[ Does it need special computers(high processing)? I use computer (linux)with RAM 32GB] If yes, would you please introduce me some valuable sites and tutorials for ORCA BEGINNER users? Best Rose On Sat, 25 Aug 2018, 18:18 Albert, wrote: > why not try some professional QM/MM software like "ORCA". It will make > your life much easier. > > > On 08/24/2018 11:54 PM, rose rahmani wrote: > > Hi, > > > > I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs. > > Since, some of these codes are commercial(like ONIOM specially > Gaussian), i > > wanted to ask are these all free in GROMACS? Or we should first register > > and by these codes separately and then use them in GROMACS? > > > > Best regards > > > > Rose > > -- > 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] gmx_dipoles Mtot and aver difference
I gave the following commands: gmx_mpi trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center (I first selected 0 and then 1, like in the lysoyme tutorial). gmx_mpi dipoles -f md_noPBC.xtc -s md.tpr Despite that, I am getting opposite values in Mtot and aver. By re-center do you mean something other than that? Looking forward to your kind help, please!! Regards, Raag -- 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] How to center my complex in the box?
Try -pbc mol and -ur compact with trjconv command. I think this will help. On Sat, Aug 25, 2018 at 7:53 PM mmousivand93 wrote: > Dear all users > > I have run a molecular dynamic simulation for my aptamer-ligand by > gromacs (50 ns), At the end of simulations,by using VMD,it seems the > molecule is out side the box, but I am not sure, is it possible to check > the attachment and explain how to center it again? > > Thanks a lot > > Maryam-- > 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. -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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] How to center my complex in the box?
Dear all users I have run a molecular dynamic simulation for my aptamer-ligand by gromacs (50 ns), At the end of simulations,by using VMD,it seems the molecule is out side the box, but I am not sure, is it possible to check the attachment and explain how to center it again? Thanks a lot Maryam-- 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] Qm/mm
why not try some professional QM/MM software like "ORCA". It will make your life much easier. On 08/24/2018 11:54 PM, rose rahmani wrote: Hi, I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs. Since, some of these codes are commercial(like ONIOM specially Gaussian), i wanted to ask are these all free in GROMACS? Or we should first register and by these codes separately and then use them in GROMACS? Best regards Rose -- 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] gmx_dipoles Mtot and aver difference
On 8/25/18 7:51 AM, Raag Saluja wrote: Hi! I had written earlier that I wanted to compare the dipole moments of a few proteins and that the Mtot and Aver files were giving me diametrically opposite results. The proteins with the highest dipole moments according to Mtot were the ones with the lowest dipole moments according to aver and vice-versa. I had asked what the difference was between the two files and why I was getting such results. David had very kindly replied that I should center the protein and had asked whether my proteins were neutral. I did use genion and -neutral command to neutralise the system. I had also centered the protein. Still I get this result. The overall charge of the *system* does not matter if you are computing the dipole properties of the *protein*. If the protein has a net charge, it must be re-center such that the center-of-charge is at the coordinate origin. -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] Qm/mm
On 8/25/18 7:09 AM, rose rahmani wrote: Sorry, what you mean exactly? You mean other free softwares or GROMACS? You have to obtain and install a suitable QM program that can do what you want and can interface with GROMACS. That's up to you to decide, and if you can't afford a license for a given QM program, you need to find a free QM code that fits those requirements. Please do be aware that the GROMACS QM/MM interface is largely unmaintained at this time, so some things may not work. -Justin On Sat, 25 Aug 2018, 02:28 Benson Muite, wrote: I believe for the non free codes, you would need to obtain a license. Depending on the calculation you want to do, there are free alternatives to the non free codes. On 08/25/2018 12:54 AM, rose rahmani wrote: Hi, I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs. Since, some of these codes are commercial(like ONIOM specially Gaussian), i wanted to ask are these all free in GROMACS? Or we should first register and by these codes separately and then use them in GROMACS? Best regards Rose -- 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 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] gmx_dipoles Mtot and aver difference
Hi! I had written earlier that I wanted to compare the dipole moments of a few proteins and that the Mtot and Aver files were giving me diametrically opposite results. The proteins with the highest dipole moments according to Mtot were the ones with the lowest dipole moments according to aver and vice-versa. I had asked what the difference was between the two files and why I was getting such results. David had very kindly replied that I should center the protein and had asked whether my proteins were neutral. I did use genion and -neutral command to neutralise the system. I had also centered the protein. Still I get this result. Looking forward to your kind help! Regards, Raag -- 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] Qm/mm
Sorry, what you mean exactly? You mean other free softwares or GROMACS? On Sat, 25 Aug 2018, 02:28 Benson Muite, wrote: > I believe for the non free codes, you would need to obtain a license. > Depending on the calculation you want to do, there are free alternatives > to the non free codes. > > > On 08/25/2018 12:54 AM, rose rahmani wrote: > > Hi, > > > > I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs. > > Since, some of these codes are commercial(like ONIOM specially > Gaussian), i > > wanted to ask are these all free in GROMACS? Or we should first register > > and by these codes separately and then use them in GROMACS? > > > > Best regards > > > > Rose > > -- > 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.
