[gmx-users] How to calculate protein-surface interaction energy
Dear users, I want to calculate the interaction energy (energy versus time) of a protein (Lysozyme) adsorption process (20ns) on to a solid surface (polyethylene). when I use gmx energy -f md.edr -o energy.xvg and then selecting total energy I end up with a messy graph!!! I am doing some wrong? secondly, Is there any way to average the energy over the last 10ns of MD trajectory in Gromacs?? Cheers James -- 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] Fwd: How to calculate protein-surface interaction energy
Dear users, I want to calculate the interaction energy (energy versus time) of a protein (Lysozyme) adsorption process (20ns) on to a solid surface (polyethylene). when I use gmx energy -f md.edr -o energy.xvg and then selecting total energy I end up with a messy graph!!! I am doing some wrong? secondly, Is there any way to average the energy over the last 10ns of MD trajectory in Gromacs?? Cheers James -- 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] Fwd: How to calculate protein-surface interaction energy
Dear users, I want to calculate the interaction energy (energy versus time) of a protein (Lysozyme) adsorption process (20ns) on to a solid surface (polyethylene). when I use gmx energy -f md20ns.edr -o energy.xvg and then selecting total energy I end up with a messy graph!!! Am I doing some thing wrong? secondly, Is there any way to average the energy over the last 10ns of MD trajectory in Gromacs?? Cheers James -- 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 calculate protein-surface interaction energy
Hi Justin, Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain a bit more what to do? if I want to have total energy= vdw and electrostatic? Cheers James On Fri, Oct 17, 2014 at 12:51 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/16/14 5:46 AM, James Lord wrote: Dear users, I want to calculate the interaction energy (energy versus time) of a protein (Lysozyme) adsorption process (20ns) on to a solid surface (polyethylene). when I use gmx energy -f md.edr -o energy.xvg and then selecting total energy I end up with a messy graph!!! I am doing some wrong? secondly, Is there any way to average the energy over the last 10ns of MD trajectory in Gromacs?? Total energy is just as it says, the total energy of the system. If you want to measure interaction energies, you need to make use of energygrps in the .mdp file to decompose (short-range) nonbonded energies. Note that the mesh term from PME is not decomposable in any straightforward way. If you did not use energygrps in the .mdp file for the run, create a new .tpr file and recalculate the energies in the existing trajectory with mdrun -rerun. -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] How to calculate protein-surface interaction energy
Hi Justin, Sorry for not being clear, I have done the simulation without specifying the energygrps, so based on your previous comment I should use mdrun -rerun trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps = Protein Surface right? If not appreciate if you give an example of the command with appropriate input output etc. Cheers James On Fri, Oct 17, 2014 at 3:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/16/14 10:47 AM, James Lord wrote: Hi Justin, Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain a bit more what to do? if I want to have total energy= vdw and electrostatic? energygrps = Protein Surface or whatever the names should be. -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] How to calculate protein-surface interaction energy
Dear Justin Diogo, Thanks for your comments, I did the steps you guys mentioned to calculate protein-suface interaction energy and expect to see protein surface option upon running g_energy but it is not the case, any comments? Here is what I did, gedit md.mdp and then added at the end of md.mdp file energygrps= protein surface saved it and grompp -f md.mdp -c mdw.gro -t mdw.cpt -p toplgy.top -o mdnew mdrun -s mdnew.tpr -rerun mdw.xtc g_energy -f mdnew.edr -o energy.xvg Thanks James On Sat, Oct 18, 2014 at 8:52 AM, Diogo Martins de Sá sadi...@mol.bio.br wrote: open your .mdp in an editor and under energygrps, add ProteinSurface after the last term. Run grompp using this .mdp and create a new .tpr. Then use the command line Justin mentioned last. Diogo -- Date: Thu, 16 Oct 2014 12:07:15 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to calculate protein-surface interaction energy Message-ID: 543fed33.5010...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 10/16/14 11:42 AM, James Lord wrote: Hi Justin, Sorry for not being clear, I have done the simulation without specifying the energygrps, so based on your previous comment I should use mdrun -rerun trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps = Protein Surface right? If not appreciate if you give an example of the command with appropriate input output etc. Create a new .tpr with the .mdp file that specifies the desired energygrps, then: mdrun -s new.tpr -rerun trj.xtc -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] How to calculate protein-surface interaction energy
Hi Justin, Thanks for the prompt answer. I selected LJ-(SR) but I am getting a positive fluctuating line over the simulation time. Looking at the vmd movie I can see that protein (Lysozyme) is coming into contact with surface afte 10ns and is 5 nm away at the beginning?? my surface is a not charged (polyethylene)?? I'd expect zero energy at beginning and upon touching the surface negative value??? any comments? Sorry this has nothing to do with Gromacs. Cheers James On Sat, Oct 18, 2014 at 11:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 6:45 AM, James Lord wrote: Dear Justin Diogo, Thanks for your comments, I did the steps you guys mentioned to calculate protein-suface interaction energy and expect to see protein surface option upon running g_energy but it is not the case, any comments? Here is what I did, gedit md.mdp and then added at the end of md.mdp file energygrps= protein surface saved it and grompp -f md.mdp -c mdw.gro -t mdw.cpt -p toplgy.top -o mdnew mdrun -s mdnew.tpr -rerun mdw.xtc g_energy -f mdnew.edr -o energy.xvg You will not see a single energy term; rather you will see both LJ and Coulombic terms like LJ-SR(Protein:Surface). -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] How to calculate protein-surface interaction energy
Hi Justin, 1. Make sure your index groups are correctly constructed. Do I need to use make ndx? I thought just adding energygrps=protein surface at the end of .mdp is enough? 2. What does 5 nm correspond to? A COM distance? A minimum distance? If the latter, then the LJ-SR energy should likely be zero, but if it's a COM distance, that's not necessarily the case. 5 nm is minimum distance 3. Is your PE model united-atom or all-atom? If the latter, you still have partial charges that will contribute to a negative Coul-SR (of course, this is something you can check very simply It is all atom Cheers James On Sun, Oct 19, 2014 at 2:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 8:51 AM, James Lord wrote: Hi Justin, Thanks for the prompt answer. I selected LJ-(SR) but I am getting a positive fluctuating line over the simulation time. Looking at the vmd movie I can see that protein (Lysozyme) is coming into contact with surface afte 10ns and is 5 nm away at the beginning?? my surface is a not charged (polyethylene)?? I'd expect zero energy at beginning and upon touching the surface negative value??? any comments? Sorry this has nothing to do with Gromacs. A few things: 1. Make sure your index groups are correctly constructed. 2. What does 5 nm correspond to? A COM distance? A minimum distance? If the latter, then the LJ-SR energy should likely be zero, but if it's a COM distance, that's not necessarily the case. 3. Is your PE model united-atom or all-atom? If the latter, you still have partial charges that will contribute to a negative Coul-SR (of course, this is something you can check very simply) -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] How to calculate protein-surface interaction energy
You are right it is the name of molecule type in .top, and thus no error upon executing grompp, so index group is constructed correctly right??? rvdw=1 nm so should be fine. and for the last part I agree. Cheers James On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 9:30 AM, James Lord wrote: Hi Justin, 1. Make sure your index groups are correctly constructed. Do I need to use make ndx? I thought just adding energygrps=protein surface at the end of .mdp is enough? Surface isn't likely a default group (unless that's the name of the [moleculetype]) and grompp should have raised a fatal error if the group wasn't defined. 2. What does 5 nm correspond to? A COM distance? A minimum distance? If the latter, then the LJ-SR energy should likely be zero, but if it's a COM distance, that's not necessarily the case. 5 nm is minimum distance OK, in this case, the initial LJ-SR should be zero, provided that rvdw 5. 3. Is your PE model united-atom or all-atom? If the latter, you still have partial charges that will contribute to a negative Coul-SR (of course, this is something you can check very simply It is all atom Then you must have partial charges on the individual atoms and therefore Coul-SR will be non-zero. -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] How to calculate protein-surface interaction energy
Hi Justin, Thanks, apparently I am doing some silly mistakes as I checked for another system I have and ended up to the same problem. I am sending all the files to your personal email and then if the problem is solved I will send a post with description of the problem and the solution to the mailing list. Is that fine with you? Cheers James On Sun, Oct 19, 2014 at 4:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 9:55 AM, James Lord wrote: You are right it is the name of molecule type in .top, and thus no error upon executing grompp, so index group is constructed correctly right??? In theory, but if you're saying that at t=0, LJ-SR is not zero, something is weird. Without access to your files, it's impossible to diagnose that any further. -Justin rvdw=1 nm so should be fine. and for the last part I agree. Cheers James On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 9:30 AM, James Lord wrote: Hi Justin, 1. Make sure your index groups are correctly constructed. Do I need to use make ndx? I thought just adding energygrps=protein surface at the end of .mdp is enough? Surface isn't likely a default group (unless that's the name of the [moleculetype]) and grompp should have raised a fatal error if the group wasn't defined. 2. What does 5 nm correspond to? A COM distance? A minimum distance? If the latter, then the LJ-SR energy should likely be zero, but if it's a COM distance, that's not necessarily the case. 5 nm is minimum distance OK, in this case, the initial LJ-SR should be zero, provided that rvdw 5. 3. Is your PE model united-atom or all-atom? If the latter, you still have partial charges that will contribute to a negative Coul-SR (of course, this is something you can check very simply It is all atom Then you must have partial charges on the individual atoms and therefore Coul-SR will be non-zero. -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. -- == 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] How to calculate protein-surface interaction energy
Hi Diogo, Yes that is what I have at the end of top file. ps: Sorry Justin I just saw your previous email. Cheers James On Sun, Oct 19, 2014 at 2:13 PM, Diogo Martins de Sá sadi...@mol.bio.br wrote: At the end of your topology file, what molecules do you have written down? You should have something like: Protein Surface SOL Ion (if you needed to equilibrate system) Diogo -- Date: Thu, 16 Oct 2014 12:07:15 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to calculate protein-surface interaction energy Message-ID: 543fed33.5010...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 10/16/14 11:42 AM, James Lord wrote: Hi Justin, Sorry for not being clear, I have done the simulation without specifying the energygrps, so based on your previous comment I should use mdrun -rerun trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps = Protein Surface right? If not appreciate if you give an example of the command with appropriate input output etc. Create a new .tpr with the .mdp file that specifies the desired energygrps, then: mdrun -s new.tpr -rerun trj.xtc -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] How to calculate protein-surface interaction energy
Hi Justin, Here is the uploaded files on 4share. http://www.4shared.com/folder/9CgRBgqp/_online.html Cheers James On Sun, Oct 19, 2014 at 2:23 PM, James Lord jjamesgreen...@gmail.com wrote: Hi Diogo, Yes that is what I have at the end of top file. ps: Sorry Justin I just saw your previous email. Cheers James On Sun, Oct 19, 2014 at 2:13 PM, Diogo Martins de Sá sadi...@mol.bio.br wrote: At the end of your topology file, what molecules do you have written down? You should have something like: Protein Surface SOL Ion (if you needed to equilibrate system) Diogo -- Date: Thu, 16 Oct 2014 12:07:15 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to calculate protein-surface interaction energy Message-ID: 543fed33.5010...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 10/16/14 11:42 AM, James Lord wrote: Hi Justin, Sorry for not being clear, I have done the simulation without specifying the energygrps, so based on your previous comment I should use mdrun -rerun trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps = Protein Surface right? If not appreciate if you give an example of the command with appropriate input output etc. Create a new .tpr with the .mdp file that specifies the desired energygrps, then: mdrun -s new.tpr -rerun trj.xtc -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] How to calculate protein-surface interaction energy
Hi Justin, Well, I tried clicking three different things that said download, but every one of them tried to download software, spam, or charge me money, so I'm going to assume that the files you sent me off-list are the same ones you've posted here. If that's not the case, please find a better place to share files. Google Docs works well. Thanks Google Docs will be used for future. How many different systems do you have? You said before you had an all-atom surface of polyethylene. This system is a united-atom layer of decane. I have protein at different liquid-solid interfaces, and I want to have interaction energy of all of them. I think I explained to you in the email with attachment why I am sending this (as I have done so many changes to protein-PE that I lost track of them) If you want people to spend time helping you, you need to provide accurate information. This system behaves correctly - there is a zero interaction energy (both Coulomb and LJ) at t=0, so it is fine. If it is correct (which when I plot the energy it is not) then I will correct the protein-PE ones. But I don't know what I'm supposed to be spending my time doing, because this isn't the system you described before as being problematic. Cheers James -Justin On Sun, Oct 19, 2014 at 4:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 10:41 PM, James Lord wrote: Hi Justin, Here is the uploaded files on 4share. http://www.4shared.com/folder/9CgRBgqp/_online.html Well, I tried clicking three different things that said download, but every one of them tried to download software, spam, or charge me money, so I'm going to assume that the files you sent me off-list are the same ones you've posted here. If that's not the case, please find a better place to share files. Google Docs works well. How many different systems do you have? You said before you had an all-atom surface of polyethylene. This system is a united-atom layer of decane. If you want people to spend time helping you, you need to provide accurate information. This system behaves correctly - there is a zero interaction energy (both Coulomb and LJ) at t=0, so it is fine. But I don't know what I'm supposed to be spending my time doing, because this isn't the system you described before as being problematic. -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] How to calculate protein-surface interaction energy
Hi Justin, Would you please tell me from the files I sent you which of them you checked and how you got to the conclusion that (I mean which command ) This system behaves correctly - there is a zero interaction energy (both Coulomb and LJ) at t=0, so it is fine. Thanks James On Mon, Oct 20, 2014 at 3:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/19/14 7:26 AM, James Lord wrote: Hi Justin, Well, I tried clicking three different things that said download, but every one of them tried to download software, spam, or charge me money, so I'm going to assume that the files you sent me off-list are the same ones you've posted here. If that's not the case, please find a better place to share files. Google Docs works well. Thanks Google Docs will be used for future. How many different systems do you have? You said before you had an all-atom surface of polyethylene. This system is a united-atom layer of decane. I have protein at different liquid-solid interfaces, and I want to have interaction energy of all of them. I think I explained to you in the email with attachment why I am sending this (as I have done so many changes to protein-PE that I lost track of them) Well you now have a reference for what should work, so hopefully that is helpful. If the PE system is giving issues, please provide *those* files so they can be diagnosed and you can get a solution. If you're having trouble keeping track of your own work, it's fairly helpless for anyone else to try ;) -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.
[gmx-users] How to obtaine different protein orientations in a biphasic system
Dear users, I have inserted a protein in a biphasic system (like Justin tutorial). My question is if I want to sample different orientations of protein to one of the phases how should I do that? I have rotated the protein with different angles (90,180,270) around X,Y,Z axes but as I have periodic boundary condition in XYZ, Am I really obtaining different orientations? any comments is appreciated Cheers James -- 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] Protein distance with respect to box walls
Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- 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] g_mindist
Dear users, I have MD of protein adsorption at an oil phase and am trying to calculate the number of residues that contact the oil at each point in time? I have tried g_mindist -f mol.xtc -s md.tpr -on numcont.xvg also with -group option but none of them gave what I am looking for. any comments?? Cheers James -- 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] Distance of residue’s centre of mass to a surface (COM)
Dear users, If I want to calculate distance of each residue's COM of a protein to a surface is g_mindist going to be my friend? It is documented that g_mindist computes the distance between one group and a number of other groups. Both the minimum distance and the number of contacts within a given distance are written to two separate output files. Cheers James -- 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] Distance of residue’s centre of mass to a surface (COM)
Hi Justin, Thanks, g_dist is calculating the centre of mass of two groups and -dist option print all atoms in group 2 closer than dist to the centre of mass of group 1, while what I am looking after is the distance of COM of residues to a surface not the centre of mass of the surface. Am I missing anything? Cheers James On Sat, Mar 28, 2015 at 1:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/15 8:03 AM, James Lord wrote: Dear users, If I want to calculate distance of each residue's COM of a protein to a surface is g_mindist going to be my friend? It is documented that g_mindist computes the distance between one group and a number of other groups. Both the minimum distance and the number of contacts within a given distance are written to two separate output files. Use g_dist, not g_mindist. -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] trjconv for cutting the trajectory in small subtrajectories
Hi Mahboobeh, I recommend checking the created trajectories with gmx check. Cheers James On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang m21.t...@qut.edu.au wrote: Hi，-e is end frame， -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) - frame 3500 time 17000.000- frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- 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. -- 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] Justin biphasic tutorial with controlled adsoption of protein
Dear gmx users, I have a biphasic system, like Justin's tutorial, but I want to control the protein to adsorb/desorb from the oil-water interface, I don't want the protein to go through oil phase just want to keep it at the interface, I have added a constant force at the end of the mdp file. i tried different pull_k1 values but what I see is, when the force is applied the oil is also deformed (which makes sense) and kinda make a hole in the oil phase and eventually pass through it. I just want to keep it at or away from the interface without deforming/puling away the oil molecules, What is the best way to do it? any suggestion? here is the mdp https://drive.google.com/open?id=0B0YMTXH1gmQsZ1ljOUZROWNGM3Mauthuser=0 cheers James -- 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] Justin biphasic tutorial with controlled adsoption of protein
Hi Justin, Thanks for the info, your assumption re long axis of the box is correct (z), here is the .gro file I have for one the oil (decane)-protein (the protein is in the middle part of the free space above the oil surface). Is that what you were talking about? I went through manual and could not get what to do for position restrains, appreciate if you can elaborate further on it? Thanks for your final point re solvent/ions separate coupling. https://drive.google.com/file/d/0B0YMTXH1gmQsYmQzRXUtN1ZENmc/view?usp=sharing Cheers James On Sun, May 3, 2015 at 4:23 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/15 10:02 AM, James Lord wrote: Dear gmx users, I have a biphasic system, like Justin's tutorial, but I want to control the protein to adsorb/desorb from the oil-water interface, I don't want the protein to go through oil phase just want to keep it at the interface, I have added a constant force at the end of the mdp file. i tried different pull_k1 values but what I see is, when the force is applied the oil is also deformed (which makes sense) and kinda make a hole in the oil phase and eventually pass through it. I just want to keep it at or away from the interface without deforming/puling away the oil molecules, What is the best way to do it? any suggestion? here is the mdp https://drive.google.com/open?id=0B0YMTXH1gmQsZ1ljOUZROWNGM3Mauthuser=0 I wouldn't use the pull code. This sounds like a task best suited for a flat-bottom restraint. I'm going to assume the long axis of the box is along z for this example. You can create a coordinate file in which the z-coordinate of all the protein atoms is equal to the middle of the box (this assumes the z dimension of the box doesn't change, e.g. semiisotropic pressure coupling with compressibility of zero along z). Then supply this file to grompp -r with a suitable [position_restraints] section that specifies a flat-bottom potential along z (see manual section 4.3.2, I think this is a case where you need a negative force constant to keep the atoms outside of the restraint region). During the run, if any protein atom hits the imaginary wall, it gets pushed back in the other direction by the flat-bottom restraint. Also, don't couple solvent and ions to separate thermostats. It's not sensible and usually not stable. -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.
[gmx-users] Area/enegy at liquid/liquid interface
Hi all, How to calculate the area occupied by a protein in atomistic simulation (I have performed the simulation already) but now want to calculate the area occupied by the protein at two liquid interfaces and also interfacial free energy reduction upon adsorption. Any detailed instructions is much appreciated. Cheers James -- 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] gromacs-5.0.4 installation problem
Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? Cheers James -- 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] gromacs-5.0.4 installation problem
Hi Mark,Szilard and Christopher, Thanks for the comments, apparently gcc 4.8.2 is there. Really can't understand why and what it is complaining about, root@ubuntu:~/gromacs-5.0.4/build# gcc --version gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So are you guys saying that a new installation might be better than messing around with this? Cheers James On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Something is strange about that Ubuntu installation, gcc 4.8.2 should be the default. -- Szilárd On Fri, May 8, 2015 at 12:10 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? Cheers James -- 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. -- 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. -- 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] gromacs-5.0.4 installation problem
YAY :-) it is working, Do not know what was wrong but apparently something was seriously messed up with cmake and compilers, removed cmake and gcc gcc++ complier and gromacs, re-doing solved the problem. *sudo apt-get update -y* *sudo apt-get update**sudo apt-get install cmake* Cheers James On Thu, May 7, 2015 at 7:45 PM, Roland Schulz rol...@utk.edu wrote: Hi, please rerun cmake from an empty build directly and post both the full cmake output and the content of CMakeFiles/CMakeError.log. Roland On Thu, May 7, 2015 at 7:38 PM, James Lord jjamesgreen...@gmail.com wrote: Hi Mark,Szilard and Christopher, Thanks for the comments, apparently gcc 4.8.2 is there. Really can't understand why and what it is complaining about, root@ubuntu:~/gromacs-5.0.4/build# gcc --version gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So are you guys saying that a new installation might be better than messing around with this? Cheers James On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Something is strange about that Ubuntu installation, gcc 4.8.2 should be the default. -- Szilárd On Fri, May 8, 2015 at 12:10 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? Cheers James -- 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. -- 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
[gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3
Dear gmx users, pdb2gmx is complaining about Incomplete ring in HIS3, for 3V03.pdb I saw Justin's comment All structures have to be complete in order for pdb2gmx to process them. The only atoms it can add are hydrogens. All heavy atoms are required. If you place the missing atom(s) correctly, according to proper geometry, you shouldn't be changing the structure too much, but a simple energy minimization after you've generated the topology should relax any poor geometry. Justin And also Florian comment on this you should take a look at the structure in your favorite viewer, perhaps some residues are missing and/ or are not resolved completly by Xray/ NMR. Take a look at REMARKS in this pdb file. Programs for modelling missing residues are: Swiss pdb viewer WHATIF pymol vmd or commercial onces: MOE Accelyrs Discovery Studio I see following remarks in the .pdb REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): 1-I also looked at the structure in VMD but how can I see the missingatoms/residues?How to know what type of atom/residues are missing? I just can see residue number 2- How to add them? Again somewhere else Justin is saying “add the missing atoms with emacs (or another text editor). Then minimize” . May I ask someone to walk me through these steps? Cheers James -- 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] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3
Hi Justin, I opened up the strucutre in Swissviewr. Then how can I have a pdb with missing parts added? Cheers James On Tuesday, May 5, 2015, Justin Lemkul jalem...@vt.edu wrote: On 5/5/15 4:32 AM, James Lord wrote: Dear gmx users, pdb2gmx is complaining about Incomplete ring in HIS3, for 3V03.pdb I saw Justin's comment All structures have to be complete in order for pdb2gmx to process them. The only atoms it can add are hydrogens. All heavy atoms are required. If you place the missing atom(s) correctly, according to proper geometry, you shouldn't be changing the structure too much, but a simple energy minimization after you've generated the topology should relax any poor geometry. Justin And also Florian comment on this you should take a look at the structure in your favorite viewer, perhaps some residues are missing and/ or are not resolved completly by Xray/ NMR. Take a look at REMARKS in this pdb file. Programs for modelling missing residues are: Swiss pdb viewer WHATIF pymol vmd or commercial onces: MOE Accelyrs Discovery Studio I see following remarks in the .pdb REMARK 465 MISSING RESIDUES Missing residues are important if they are internal or otherwise important for function. Frequently, terminal residues are disordered and cannot be resolved by crystallography. REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; Here's the most important section of your PDB file (at least, in this context): REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 3CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 4CE NZ REMARK 470 LYS A 41CD CE NZ REMARK 470 LYS A 76CE NZ ... You have hundreds and hundreds of missing atoms in this structure. They need to be modeled back or there will be no way to produce a topology. REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): 1-I also looked at the structure in VMD but how can I see the missingatoms/residues?How to know what type of atom/residues are missing? I just can see residue number Read the contents of the PDB file, i.e. the snippet that I posted. 2- How to add them? Again somewhere else Justin is saying “add the missing atoms with emacs (or another text editor). Then minimize” . This certainly doesn't apply to you. If you're missing an atom or two, it's trivial to calculate where they should be based on existing atoms. In your case, you have a huge amount of missing atoms. Try SwissPDBViewer (which adds back missing atoms as soon as you open the file - convenient!) or anything else you might like (I think WHATIF can do this, too, but I've never done it). -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] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3
Many thanks Justin, I created a new .pdb file with SwissPDBViewr but again executing pbd2gmx is giving the following warning and error Warning: Starting residue CA584 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA585 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA586 in chain not identified as Protein/RNA/DNA. Warning: Starting residue ACT587 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION -4.5.4 Source code file: /home/James/gromacs-4.5.4/src/kernel/resall.c, line: 642 Fatal error: Residue 'ACT' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Here is the link to new PDB, my question is what is ACT residue? and how to resolve this issue, any thought is greatly appreciated? https://drive.google.com/file/d/0B0YMTXH1gmQsSWlXTU56R0FYcVk/view?usp=sharing Cheers James On Sat, May 9, 2015 at 12:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/9/15 3:13 AM, James Lord wrote: Hi Justin, I opened up the strucutre in Swissviewr. Then how can I have a pdb with missing parts added? It's done automatically. You should see a window pop up indicating missing atoms and that they have been built back. Then just save the .pdb file. There are tutorials online for this and you should consult whatever documentation and help forums SwissPDBViewer may provide. -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] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3
Thanks Justin. On Wed, May 13, 2015 at 11:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/13/15 6:16 AM, James Lord wrote: Many thanks Justin, I created a new .pdb file with SwissPDBViewr but again executing pbd2gmx is giving the following warning and error Warning: Starting residue CA584 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA585 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA586 in chain not identified as Protein/RNA/DNA. Warning: Starting residue ACT587 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION -4.5.4 Source code file: /home/James/gromacs-4.5.4/src/kernel/resall.c, line: 642 Fatal error: Residue 'ACT' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Here is the link to new PDB, my question is what is ACT residue? and how to Did you read the contents of the PDB file? REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CA ACETATE, 20% PEG3350, 0.1 M REMARK 280 TRIS HCL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K If you visualize ACT you will see it is acetate. resolve this issue, any thought is greatly appreciated? Given that it's a crystallization co-solvent it's unlikely to be functional in any way, so you can likely delete it. -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.
[gmx-users] total charge (qtot)
Dear gmx users, I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb, https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing I would like to know the total charge of my system but I have two statement for that,after running pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce one is saying -9e and 2e? I am a bit confuse can anyone tell me why it is like this? I also checked the topol.top and there is no qtot pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 1HFX.pdb InputStructure file: gro g96 pdb tpr etc. -o 1HFX_processed.gro Output Structure file: gro g96 pdb etc. -p topol.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id or interactive -merge enum no Merge multiple chains into a single [moleculetype]: no, all or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum spceWater model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, instead of charged (default) -[no]lys bool no Interactive lysine selection, instead of charged -[no]arg bool no Interactive arginine selection, instead of charged -[no]asp bool no Interactive aspartic acid selection, instead of charged -[no]glu bool no Interactive glutamic acid selection, instead of charged -[no]gln bool no Interactive glutamine selection, instead of neutral -[no]his bool no Interactive histidine selection, instead of checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the coordinate file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the .rtp file -[no]cmapbool yes Use cmap torsions (if enabled in the .rtp file) -[no]renum bool no Renumber the
Re: [gmx-users] total charge (qtot)
I can see that I have two chains but can I simply say the total charge is -7 e? Cheers James On Thu, May 14, 2015 at 1:04 AM, James Lord jjamesgreen...@gmail.com wrote: Dear gmx users, I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb, https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing I would like to know the total charge of my system but I have two statement for that,after running pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce one is saying -9e and 2e? I am a bit confuse can anyone tell me why it is like this? I also checked the topol.top and there is no qtot pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 1HFX.pdb InputStructure file: gro g96 pdb tpr etc. -o 1HFX_processed.gro Output Structure file: gro g96 pdb etc. -p topol.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id or interactive -merge enum no Merge multiple chains into a single [moleculetype]: no, all or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum spceWater model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, instead of charged (default) -[no]lys bool no Interactive lysine selection, instead of charged -[no]arg bool no Interactive arginine selection, instead of charged -[no]asp bool no Interactive aspartic acid selection, instead of charged -[no]glu bool no Interactive glutamic acid selection, instead of charged -[no]gln bool no Interactive glutamine selection, instead of neutral -[no]his bool no Interactive histidine selection, instead of checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the coordinate file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen
Re: [gmx-users] genion error sol not continuous
Hi Justin, Thanks for your email. I have modified it and the topology looks fine to me or at least I can't see any problem with it but still genion does not like it? Would please have a look? https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing https://drive.google.com/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing Thanks James On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 1:25 AM, James Lord wrote: Hi all, I am trying to neutralize this system (1HFX.gro) and genion is complaining about solvent not being continuous,then I made the 1HFX_modified.gro in which I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end of the file. I am expecting gromacs to do the reordering for SOL. Am I missing anything? The topology needs to be modified in a similar manner. IIRC it is topological continuity that genion checks. -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] Forced adsoprtion and desorption of a protein on a surface
Thanks heaps mastermind Justin. James On Thursday, April 9, 2015, Justin Lemkul jalem...@vt.edu wrote: On 4/9/15 2:45 AM, James Lord wrote: Dear Users, I am wondering if anyone can help me out with forced adsorption/ desorption of a protein on surface. I am aware of pulling code in Justin's tutorial but that is not what I am looking for. I want a simple constant force (perpendicular to the surface) method to push and/or pull the protein (center of mass) onto /or from a surface at specific time intervals during the simulation . Appreciate any comments. There's no way to tell mdrun to apply the pull code only during given time intervals, so you'd have to run for some time, create a new .tpr that contains pulling instructions to continue while applying the biasing potential, turn off the pull code or change it, repeat as needed. -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.
[gmx-users] Forced adsoprtion and desorption of a protein on a surface
Dear Users, I am wondering if anyone can help me out with forced adsorption/ desorption of a protein on surface. I am aware of pulling code in Justin's tutorial but that is not what I am looking for. I want a simple constant force (perpendicular to the surface) method to push and/or pull the protein (center of mass) onto /or from a surface at specific time intervals during the simulation . Appreciate any comments. Cheers James -- 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] Biphasic Systems for BSA
Hi all, I have a trivial question, What is the best box type and size for a big protein such as BSA (attached .pdb) to minimize computational cost? what is the rule of thumb re the protein distance to box wall? This protein is around 16 nm in x direction and 6nm in y. https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view?usp=sharing Cheers James -- 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] energy minimization error
Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * *Cheers* *James* On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com wrote: Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -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] energy minimization error
Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -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] Biphasic Systems for BSA
Hi Justin Tsjerk, Thanks for the info, Tsjerk: I was looking for the monomer but could not find monomer structure on protein data bank. Cheers James On Sun, Jun 28, 2015 at 6:50 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, Actually no, you may be better off with a hexagonal prism, or even a rhombic dodecahedron, which has a hexagonal base too. Oh, and that structure of BSA is a dimer, while the biological unit is a monomer... Cheers, Tsjerk On Jun 27, 2015 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/15 2:38 AM, James Lord wrote: Hi all, I have a trivial question, What is the best box type and size for a big protein such as BSA (attached .pdb) to minimize computational cost? what is the rule of thumb re the protein distance to box wall? This protein is around 16 nm in x direction and 6nm in y. https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view?usp=sharing If, as your subject line implies, you are setting up a layered system, you are largely stuck with a rectangular box. The dimensions can easily be determined by setting up the protein in a cubic box with editconf and conventional solute-box distances. That distance depends on the force field (viz. the required cutoffs), to avoid minimum-image violations. This is all very rudimentary stuff and is covered by tutorials and MD texts. -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. -- 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] Biphasic Systems for BSA
Hi Justin, Thanks for your email. Would you please tell me how I can do this? Sorry to bother you. below is the PBD I generated with Swiss-PdbViewr. https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view On Sun, Jun 28, 2015 at 11:47 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/15 7:46 PM, James Lord wrote: Hi Justin Tsjerk, Thanks for the info, Tsjerk: I was looking for the monomer but could not find monomer structure on protein data bank. Because it crystallizes as a dimer. The state in the crystal is not necessarily what one finds in solution. Just pull a single chain out of the PDB file. -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] Biphasic Systems for BSA
Thanks heaps Justin On Sun, Jun 28, 2015 at 1:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/15 9:48 PM, James Lord wrote: Hi Justin, Thanks for your email. Would you please tell me how I can do this? Sorry to bother you. below is the PBD I generated with Swiss-PdbViewr. https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view This is very simple with standard Linux command-line tools, e.g. to get monomer chain A: grep A 3V03.pdb | grep ATOM\|HETATM chainA.pdb -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.
[gmx-users] GPU gromacs
Hi All, I have a system with 300k atoms, I don't have access to HPC facilities, Is it possible to run gromcas on GPU on a desktop with following graphic card for up to 200-300 ns? 00:02.0 VGA compatible controller: Intel Corporation 3rd Gen Core processor Graphics Controller (rev 09) 01:00.0 VGA compatible controller: NVIDIA Corporation GF108M [GeForce GT 635M] (rev a1) any thoughts is greatly appreciated. Cheers James -- 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] Fwd: Question about editconf -noc flag
Hi all, I have made an oil slab (energy minimized, equilibrated nvt and npt), some of the oil molecules are at the other end (periodicity). https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs then I decided to increase the box size in z direction a bit to make enough room for protein, using editconf -f OCT_npt.gro -oOCT_newbox.gro -box 6.47271 6.47271 16 -noc https://drive.google.com/open?id=0B0YMTXH1gmQsT1M3dzBNNTJrT28 I used the last flag to put the oil at the ends of box but it is not doing for one end? any thoughts? Cheers James -- 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] editconf -density
Hi all, I have a solvent filled in a box of dimensions 12 12 12 (solv_large.gro). I want to adjust the density of system to 824 kg/m3. But I want editconf to just change the volume only by changing the z direction ? is that possible? I did ediftconf -f solv_large.gro -o solv_large_scaled.gro -density 824 But it changes the x,y,z to adjust the density. Is it possible to ask editconf to do this only by changing for example z? Cheers James -- 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] Gromos 53a6, .mdp parameters for reaction field
Hi Mohsen, I am struggling with the same problem would you mind if I ask you to send me your .mdp file ? Cheers James On Tue, Aug 11, 2015 at 4:00 AM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: As an update, After reading the suggested links I tried two .mdp files which were suggested in discussions as solutions. Both worked without any problem on my system. 1) rlist/r(columb/vdw)=(1.4/1.4) , in fact the problem seems to be the twin-range + RF 2) I used twin-range + RF BUT I reduced the nstlist to 1, this also works for my system. Thanks for your comments. Cheers Mohsen On Tue, Jul 21, 2015 at 4:44 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: I looked at the first link, it was a useful discussion. Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and everything is working properly till now. It seems the problem was the twin-range + RF with this version of Gromacs as has been discussed and you mentioned already. I am playing a little bit to see if I everything will be fine with the rest of test simulation. I will reply again after my tests. Thanks for the links Cheers Mohsen On Tue, Jul 21, 2015 at 4:21 PM, João M. Damas jmda...@itqb.unl.pt wrote: I really think you may be losing time with LINCS parameters. Look at these links too: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html http://redmine.gromacs.org/issues/1400 You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really think that this may be the source of your problems. The links that I sent you present solutions to your problem, but almost always at a computational cost, i.e. slower simulations. João On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban vvcha...@gmail.com wrote: Maybe indeed downgrade to an earlier version. I, for sure, successfully used reaction field with gromacs 3-3-3 (imagine when it was). Professor Vitaly V. Chaban On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated structures again cause LINCS problems in one not in the other one. I have tried lincs-iter and lincs-order and also lincs allowable angle deviations but LINCS error still exist. This is why I think there is something wrong with other parameters, e.g. reaction field! Sure, I will look at epsilon_r, thanks. On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0
Re: [gmx-users] Gromacs Path
Hi Vikas, typing mdrun or which mdrun in your terminal will tell you where it is installed. Cheers James On Monday, July 27, 2015, Live King vikasdubey1...@gmail.com wrote: Hi Everyone, I installed Gromacs-4.6.5 using the command sudo apt-get install gromacs, then what is path of my Gromacs directory ? I don't seem to find it anywhere . Thanks, vikas -- 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 javascript:;. -- 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] Question about biphasic tutorial
Hi Justin, Welcome back. Thanks I solved it the other day. I got the coordinate and topology. Cheers James On Monday, July 27, 2015, Justin Lemkul jalem...@vt.edu wrote: On 7/24/15 4:16 AM, James Lord wrote: Hi all, I want to make the the hydrophobic layer Justin has made but only have one .itp file from ATB for the hydrophobic layer (no topology and coordinate)? Any suggestion where and how to start to make this hydrophobic layer? I am aware of what Justin has suggested regarding using PRODRG http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg,. any comments? I really don't understand what you're asking. Can you explain your intended process in more detail? -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.
[gmx-users] Question about biphasic tutorial
Hi all, I want to make the the hydrophobic layer Justin has made but only have one .itp file from ATB for the hydrophobic layer (no topology and coordinate)? Any suggestion where and how to start to make this hydrophobic layer? I am aware of what Justin has suggested regarding using PRODRG http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg,. any comments? Cheers James -- 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] Fwd: itp file not found
Hi all, I am running energy minimization and grompp is complaining about following error. I am using Gromacs version 4.6.3. On Gromacs website it is saying that GROMOS96 54A7 files from ATB website were added to 4.6.2 and later versions right? http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=TOLnFV9q38vJudxw-JZkbI7m1r4rIAoHfY4Juci2q9ENk7mUf5LSCGgAdAB0AHAAOgAvAC8AdwB3AHcALgBnAHIAbwBtAGEAYwBzAC4AbwByAGcALwBBAGIAbwB1AHQAXwBHAHIAbwBtAGEAYwBzAC8AUgBlAGwAZQBhAHMAZQBfAE4AbwB0AGUAcwAvAFYAZQByAHMAaQBvAG4AcwBfADQALgA2AC4AeAA.URL=http%3a%2f%2fwww.gromacs.org%2fAbout_Gromacs%2fRelease_Notes%2fVersions_4.6.x Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293 Fatal error: Topology include file ffG54a7.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors My first question is why this .itp file can't be located by grompp? I tried to bypass it and downloaded the gromos54a7.ff from ATB ( GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=cxl2s6da--E--3Qm8eDeHLVMVJnO0awk6_wjHfUmuHINk7mUf5LSCGgAdAB0AHAAOgAvAC8AYwBvAG0AcABiAGkAbwAuAGIAaQBvAHMAYwBpAC4AdQBxAC4AZQBkAHUALgBhAHUALwBhAHQAYgAvAGYAbwByAGMAZQBmAGkAZQBsAGQAXwBmAGkAbABlAHMALwBhAHQAYgBfAGcAcgBvAG0AYQBjAHMALwA1AC8AZwByAG8AbQBvAHMANQA0AGEANwBfAGEAdABiAC4AZgBmAC4AdABhAHIALgBnAHoAURL=http%3a%2f%2fcompbio.biosci.uq.edu.au%2fatb%2fforcefield_files%2fatb_gromacs%2f5%2fgromos54a7_atb.ff.tar.gz ) and extracted the force field and put it in my working directory. but again grompp is not happy??!! Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734 Fatal error: Syntax error - File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors the topology file and the included decane_G54A7.itp file in line 4 are uploaded. Any thought would be greatly appreciated. https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing%20https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing%20https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing Cheers James -- 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] itp file not found
Hi all, I am running energy minimization and grompp is complaining about following error. I am using Gromacs version 4.6.3. On Gromacs website it is saying that GROMOS96 54A7 files from ATB website were added to 4.6.2 and later versions right? http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=TOLnFV9q38vJudxw-JZkbI7m1r4rIAoHfY4Juci2q9ENk7mUf5LSCGgAdAB0AHAAOgAvAC8AdwB3AHcALgBnAHIAbwBtAGEAYwBzAC4AbwByAGcALwBBAGIAbwB1AHQAXwBHAHIAbwBtAGEAYwBzAC8AUgBlAGwAZQBhAHMAZQBfAE4AbwB0AGUAcwAvAFYAZQByAHMAaQBvAG4AcwBfADQALgA2AC4AeAA.URL=http%3a%2f%2fwww.gromacs.org%2fAbout_Gromacs%2fRelease_Notes%2fVersions_4.6.x Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293 Fatal error: Topology include file ffG54a7.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors My first question is why this .itp file can't be located by grompp? I tried to bypass it and downloaded the gromos54a7.ff from ATB ( GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=cxl2s6da--E--3Qm8eDeHLVMVJnO0awk6_wjHfUmuHINk7mUf5LSCGgAdAB0AHAAOgAvAC8AYwBvAG0AcABiAGkAbwAuAGIAaQBvAHMAYwBpAC4AdQBxAC4AZQBkAHUALgBhAHUALwBhAHQAYgAvAGYAbwByAGMAZQBmAGkAZQBsAGQAXwBmAGkAbABlAHMALwBhAHQAYgBfAGcAcgBvAG0AYQBjAHMALwA1AC8AZwByAG8AbQBvAHMANQA0AGEANwBfAGEAdABiAC4AZgBmAC4AdABhAHIALgBnAHoAURL=http%3a%2f%2fcompbio.biosci.uq.edu.au%2fatb%2fforcefield_files%2fatb_gromacs%2f5%2fgromos54a7_atb.ff.tar.gz ) and extracted the force field and put it in my working directory. but again grompp is not happy??!! Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734 Fatal error: Syntax error - File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors the topology file and the included decane_G54A7.itp file in line 4 are uploaded. Any thought would be greatly appreciated. https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing Cheers James -- 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] Fwd: itp file not found
Hi all, Sorry apparently my previous emails the shared links just contained one file, apologize for that. I am running energy minimization and grompp is complaining about following error. I am using Gromacs version 4.6.3. On Gromacs website it is saying that GROMOS96 54A7 files from ATB website were added to 4.6.2 and later versions right? http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=TOLnFV9q38vJudxw-JZkbI7m1r4rIAoHfY4Juci2q9ENk7mUf5LSCGgAdAB0AHAAOgAvAC8AdwB3AHcALgBnAHIAbwBtAGEAYwBzAC4AbwByAGcALwBBAGIAbwB1AHQAXwBHAHIAbwBtAGEAYwBzAC8AUgBlAGwAZQBhAHMAZQBfAE4AbwB0AGUAcwAvAFYAZQByAHMAaQBvAG4AcwBfADQALgA2AC4AeAA.URL=http%3a%2f%2fwww.gromacs.org%2fAbout_Gromacs%2fRelease_Notes%2fVersions_4.6.x Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293 Fatal error: Topology include file ffG54a7.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors My first question is why this .itp file can't be located by grompp? I tried to bypass it and downloaded the gromos54a7.ff from ATB ( GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=cxl2s6da--E--3Qm8eDeHLVMVJnO0awk6_wjHfUmuHINk7mUf5LSCGgAdAB0AHAAOgAvAC8AYwBvAG0AcABiAGkAbwAuAGIAaQBvAHMAYwBpAC4AdQBxAC4AZQBkAHUALgBhAHUALwBhAHQAYgAvAGYAbwByAGMAZQBmAGkAZQBsAGQAXwBmAGkAbABlAHMALwBhAHQAYgBfAGcAcgBvAG0AYQBjAHMALwA1AC8AZwByAG8AbQBvAHMANQA0AGEANwBfAGEAdABiAC4AZgBmAC4AdABhAHIALgBnAHoAURL=http%3a%2f%2fcompbio.biosci.uq.edu.au%2fatb%2fforcefield_files%2fatb_gromacs%2f5%2fgromos54a7_atb.ff.tar.gz ) and extracted the force field and put it in my working directory. but again grompp is not happy??!! Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734 Fatal error: Syntax error - File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors the topology file and the included decane_G54A7.itp file in line 4 are uploaded. Any thought would be greatly appreciated. https://drive.google.com/open?id=0B0YMTXH1gmQscndZcVJxZnZGU2M https://drive.google.com/open?id=0B0YMTXH1gmQsVGV0WXBSMU1GbFU Cheers James -- 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] Fwd: hydrogen bonds
Hi all, I am trying to figure out the number of hydrogen bonds between a protein and membrane and which residues from protein were involved in hydrogen bonding. I made an index file and selected the protein and membrane, g_hbond -f md.xtc -s md.tpr -n index.ndx -num hbond.xvg -hbn hbond.ndx the hbond.xvg is giving me the number of hydrogen bonds and as far as I understood from manual hbond.ndx is should give me the atoms involved but I am confused seeing the output of hbond.ndx. What are the three columns at the end (atom numbers involved in hydrogen bonding)? Any comments? [ hbonds_Protein-MEM ] 1 2 6407 1 2 7982 1 2 7988 161162 4391 201202 4391 201202 4523 201202 5153 201202 5174 201202 5676 201202 5678 253254 3137 266267 3131 266267 5903 275276 3131 275276 5903 279280 3257 279280 3258 279280 3261 279280 3263 279280 5903 279280 5909 279280 8864 301302 2375 310311 3257 310311 3258 310311 3263 310311 3284 316317 3284 323324 2375 323324 2402 323324 3257 323324 3258 323324 3261 323324 3263 323324 3282 323324 3284 323324 5909 323324 6974 323324 6975 323324 6999 323324 7001 323324 8675 323324 8676 323324 8702 323324 8864 323324 8865 323324 8868 323324 8870 323324 8889 323324 8891 332333 2402 332333 8681 332333 8702 332333 8864 332333 8865 332333 8868 332333 8870 332333 8889 332333 8891 336337 2375 336337 2402 364365 2402 367368 2400 367368 2402 367368 8702 370371 2402 370371 8702 606607 8045 606607 8681 606607 8864 606607 8865 606607 8868 606607 8870 606607 8889 606607 8891 630631 8675 630631 8681 630631 8702 974975 7043 987988 6218 987988 6219 987988 6224 987988 6245 1131 1132 1809 1131 1132 1833 1131 1132 3131 1131 1132 3132 1131 1132 3135 1131 1132 3137 1131 1132 3158 1131 1132 6407 1131 1132 6413 1226 1227 4418 1226 1227 4517 1226 1227 6218 1226 1227 6245 1238 1239 4418 1238 1239 4517 1248 1249 4517 1248 1249 6224 1265 1266 6219 1299 1300 4859 1339 1340 4859 1355 1356 3320 1355 1356 3509 1355 1356 3510 1355 1356 3513 1355 1356 3515 1355 1356 4017 1355 1356 4019 1355 1356 4040 1355 1356 4838 1355 1356 7799 1383 1384 2501 1383 1384 3137 1383 1384 3158 1383 1384 3515 1383 1384 3536 1383 1384 4019 1383 1384 7169 1383 1384 7799 1383 1384 7982 1389 1390 7982 1395 1396 4013 1411 1412 3132 1411 1412 4013 1411 1412 4019 1428 1429 1808 1428 1429 1835 1428 1429 3131 1428 1429 3132 1428 1429 3135 1428 1429 3137 1428 1429 3156 1428 1429 3158 1428 1429 5930 1441 1442 3257 1447 1448 3131 1447 1448 3132 1447 1448 4013 1447 1448 4017 1447 1448 4019 1447 1448 4859 1450 1451 3131 1450 1451 3132 1450 1451 3135 1450 1451 3137 1450 1451 4013 1450 1451 4014 1450 1451 4017 1450 1451 4019 1450 1451 4838 1450 1451 4859 1453 1454 3131 1453 1454 3132 1453 1454 3137 1453 1454 3156 1453 1454 4013 1453 1454 4014 1453 1454 4017 1453 1454 4019 1453 1454 4859 1467 1468 2375 1467 1468 2379 1467 1468 3257 1467 1468 3258 1467 1468 3284 1471 1472 2375 1471 1472 2379 1471 1472 3257 1471 1472 3282 1471 1472 3284 1498 1499 4518 1498 1499 4523 1498 1499 5090 1498 1499 6180 1498 1499 6182 1510 1511 6182 1514 1515 4523 1514 1515 5153 1514 1515 5174 1514 1515 6182 1514 1515 6281 1514 1515 6287 1526 1527 4523 1526 1527 5084 1526 1527 5085 1526 1527 5088 1526 1527 5090 1526 1527 5111 1526 1527 5147 1526 1527 5148 1526 1527 5151 1526 1527 5153 1526 1527 5172 1526 1527 5174 1526 1527 6156 1526 1527 6180 1526 1527 6182 1526
[gmx-users] Question regarding box size
Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce the box size? If yes how? (the .gro file is uploaded). I know from Justin tutorial genconf -nboxvector 1 1 1 Does the numbers after -nbox have to integer? The size of box required to contain protein with 1.5nm of water on each side. Sorry I could not figure it out what to do and how to tackle this simple task. re bulding the simulation from scratch is an option but thought might find quicker and smarter way here. I want to have optimum size in each direction so that the protein does not see its periodic image. Appreciate any specific thoughts on my system and the box size I have got now. https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing Cheers James -- 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] Question regarding box size
Thanks Justin and Victor On Sat, Jul 11, 2015 at 9:12 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/15 1:35 AM, James Lord wrote: Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce the box size? If yes how? (the .gro file is uploaded). I know from Justin tutorial genconf -nboxvector 1 1 1 Does the numbers after -nbox have to integer? The size of box required to contain protein with 1.5nm of water on each side. Sorry I could not figure it out what to do and how to tackle this simple task. re bulding the simulation from scratch is an option but thought might find quicker and smarter way here. I want to have optimum size in each direction so that the protein does not see its periodic image. Appreciate any specific thoughts on my system and the box size I have got now. https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing Given that you have a large protein and you're creating a biphasic system, there's not much you can do. The water box may be a bit large along z, but that's about all you can likely change here. -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] GPU gromacs
Thanks Slizard. I need to get this simulation done in a week but does not have the right facilities. Is there anyone in the group with some high end GPU cards that can help me get this running. Cheers James On Tuesday, July 7, 2015, Szilárd Páll pall.szil...@gmail.com wrote: Of course you can, but with such a low-end mobile GPU you may not even gain performance from offloading computation from the CPU and additionally you may have issues with cooling too. You can simply try comparing performance with -nb cpu and -nb gpu to see if using the GPU improves performance at all. -- Szilárd On Sat, Jul 4, 2015 at 1:40 PM, James Lord jjamesgreen...@gmail.com javascript:; wrote: Hi All, I have a system with 300k atoms, I don't have access to HPC facilities, Is it possible to run gromcas on GPU on a desktop with following graphic card for up to 200-300 ns? 00:02.0 VGA compatible controller: Intel Corporation 3rd Gen Core processor Graphics Controller (rev 09) 01:00.0 VGA compatible controller: NVIDIA Corporation GF108M [GeForce GT 635M] (rev a1) any thoughts is greatly appreciated. Cheers James -- 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 javascript:;. -- 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 javascript:;. -- 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] biphasic simulation and surface-surface tension calculation
Hi all, I have done two simulations following Justin's tutorial for biphasic systems one with cyclohexane-water and the other one with a protein in water phase that diffuses and comes to the cyclohexane-water interface at some points and stays there for the rest of simulation. When I calculate the surface tension as a function of time for cyclohexane-water system it fluctuates a lot but when I average it over the time of simulation it is giving me a reasonable value which matches with experimental one. But for the simulation that I have protein, it is again just giving me the surface tension of two liquids while I was expecting the surface tension to decrease upon protein adsorption at interface (this is the case experimentally, as the protein acts like a surfactant)? Does anyone have experience with such a system? any comments is much appreciated. Here is what I am doing to get surface-surface tension g_energy -f energy.edr -s md.tpr -o surften.xvg selecting #Surf*SurfTen when asked Cheers James -- 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] force fields selection
Hi Antonio, Thanks for further information and the paper. Cheers James On Thu, Sep 24, 2015 at 3:30 AM, Antonio Baptista <bapti...@itqb.unl.pt> wrote: > On Tue, 22 Sep 2015, Justin Lemkul wrote: > > >> >> On 9/21/15 10:22 PM, James Lord wrote: >> >>> Dear gmx users, >>> >>> I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein >>> partitioning at biphasic liquid-liquid interfaces (Similar Justin's >>> tutorial for biphasic system). Which one is recommended if anyone has >>> experience with such system and why? appreciate any comments? I know 54a7 >>> is newer version but does it mean it is the best I mean in terms of >>> reproducing experimental data etc? or is there any well known problems >>> with >>> 43a2 for such a system? >>> >>> >> 54a7 corrected a well-known problem in 53a6 with helices being unstable. >> Previous version (45a3, 43a1, etc) did not have that problem. >> > > If you are concerned with helix stability and/or dynamics, 54a7 is > probably a good choice. For example, it reproduces the thermodynamics and > kinetics of a model peptide used in helix nucleation studies: > http://dx.doi.org/10.1021/ct400529k > > > >> -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. > -- 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] force fields selection
Dear gmx users, I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein partitioning at biphasic liquid-liquid interfaces (Similar Justin's tutorial for biphasic system). Which one is recommended if anyone has experience with such system and why? appreciate any comments? I know 54a7 is newer version but does it mean it is the best I mean in terms of reproducing experimental data etc? or is there any well known problems with 43a2 for such a system? Cheers James -- 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] Fwd: removing some atoms
Hi all, I sent this few days ago and I am still struggling with this, any help,hints is highly appreciated. -- Forwarded message -- From: James Lord <jjamesgreen...@gmail.com> Date: Thu, Nov 26, 2015 at 11:18 PM Subject: removing some atoms To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> Hi all, I have a oil slab and want to insert a protein so that almost half of the protein is inserted into the oil and the other half is outside in the vacuum. Is there any tools in Gromacs so that I can easily remove some of the oil atoms and make a space for the protein insertion? My apology if it seems a trivial question. Cheers, James -- 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] removing some atoms
Hi all, I have a oil slab and want to insert a protein so that almost half of the protein is inserted into the oil and the other half is outside in the vacuum. Is there any tools in Gromacs so that I can easily remove some of the oil atoms and make a space for the protein insertion? My apology if it seems a trivial question. Cheers, James -- 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.
