Re: [gmx-users] protein -ligand complex dissociating during simulation
On Sat, 22 Jul 2017 at 2:47 AM, Justin Lemkul wrote: > > > On 7/21/17 10:56 AM, RAHUL SURESH wrote: > > It sounds like some internal dihedral problem. Request you, check on it. > > > > How did you deduce that? Dear Justin I faced the similar kind of problem. Visualisation Of my trajectory helped me a lot in solving this issue. I had to reparameterize the topology of ligand to overcome this error. Thank you > > > Indeed, conformational sampling may be an issue, so one should check the > internal geometries of the ligands, preservation of various interactions > with > the protein (H-bonding and other characteristic distances and angles, etc). > Revisit your parametrization, if you used some black-box method without > validation and/or refinement, you may just have a junk ligand topology. > > -Justin > > > On Fri, 21 Jul 2017 at 6:54 PM, Sneha Vishwanath < > > snehavishwanat...@gmail.com> wrote: > > > >> @ Justin: I have re-imaged the trajectory with trjconv using and still > the > >> ligand dissociates from one of the chain but remain bound with the other > >> chain. > >> > >> @ Gangotri: I am not sure how constraining the bond between protein > might > >> help. Can you please elaborate if possible. > >> > >> Thanks in advance. > >> > >> Sneha > >> > >> On Fri, Jul 21, 2017 at 6:37 PM, Justin Lemkul wrote: > >> > >>> > >>> > >>> On 7/21/17 8:56 AM, Sneha Vishwanath wrote: > >>> > Dear all > > I am simulating a dimeric protein, with each subunit bound to a small > molecule. During the simulation, one of the ligands is dissociating > from > the chain and moving all around the chain while the same ligand > remains > bound to the chain during simulation. Experiments show that the ligand > binds to both the subunit which is further supported by the > experimental > structure of the protein-ligand complex (which I have used for the > simulation). The simulation is for 50 ns and it usually starts > dissociating > after 10 ns. > > Any thoughts on why could it be happening and how it can be > >> circumvented? > Any help would be useful. > > > >>> Are you sure this is not simply a PBC artifact? Have you > >>> re-imaged/centered the trajectory appropriately with trjconv? > >>> > >>> -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. > >> > > -- > == > > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] Did -ndec stop working in 2016 releases?
Hi, The g96 format is useful for this purpose. Mark On Fri, 21 Jul 2017 23:18 Caro Miguel wrote: > Thanks, that clarifies it (my bad!). > > > -- > Dr. Miguel Caro > Postdoctoral researcher > Department of Electrical Engineering and Automation, and > COMP Centre of Excellence in Computational Nanoscience > Aalto University, Finland > Email: mcar...@gmail.com > Work: miguel.c...@aalto.fi > Website: http://mcaroba.dyndns.org > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin > Lemkul > Sent: 22 July 2017 00:14:10 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Did -ndec stop working in 2016 releases? > > > > On 7/21/17 5:11 PM, Caro Miguel wrote: > > Hello, > > > > > > I am trying to extract trajectory data with more decimal places than the > standard. I have been using gmx trjconv with the -ndec option to do this in > the past. I am now using the 2016.3 release and the following command: > > > > > > gmx trjconv -f md.trr -s md.tpr -o traj.gro -ndec 5 > > > > > > gives me a traj.gro file with only 3 decimal places, which is the > default. I have also tested the 2016.1 release and I experience the same > problem. Gromacs 5.1.4 behaves as expected. > > > > > > Apparently trjconv understands -ndec since it's telling me "Setting > output precision to 1e-05 (nm)", but the output .gro file is missing more > decimal digits. Is this a (known) bug or should I be looking for problems > with my installation? > > > > This is by design. Release notes are the first port of call! > > > http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/release-notes.html#removed-variable-precision-gro-writing > > -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] Regarding creating a box around the molecule and neutralization of charge before EM and MD
On 7/21/17 9:58 AM, S M Bargeen Turzo wrote: In order to do an energy minimization and md simulation is it a must to create a box around your molecule of interest(whether it be a small or macro molecule). If so can you please explain why? Depends on what you want to model. If you want to simulate in the condensed phase, generally a box full of water is necessary. Neutralizing ions aren't strictly necessary with PME due to the neutralizing background plasma, but is required in many heterogeneous environments due to artifacts with that approach. -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.
Re: [gmx-users] Did -ndec stop working in 2016 releases?
Thanks, that clarifies it (my bad!). -- Dr. Miguel Caro Postdoctoral researcher Department of Electrical Engineering and Automation, and COMP Centre of Excellence in Computational Nanoscience Aalto University, Finland Email: mcar...@gmail.com Work: miguel.c...@aalto.fi Website: http://mcaroba.dyndns.org From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: 22 July 2017 00:14:10 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Did -ndec stop working in 2016 releases? On 7/21/17 5:11 PM, Caro Miguel wrote: > Hello, > > > I am trying to extract trajectory data with more decimal places than the > standard. I have been using gmx trjconv with the -ndec option to do this in > the past. I am now using the 2016.3 release and the following command: > > > gmx trjconv -f md.trr -s md.tpr -o traj.gro -ndec 5 > > > gives me a traj.gro file with only 3 decimal places, which is the default. I > have also tested the 2016.1 release and I experience the same problem. > Gromacs 5.1.4 behaves as expected. > > > Apparently trjconv understands -ndec since it's telling me "Setting output > precision to 1e-05 (nm)", but the output .gro file is missing more decimal > digits. Is this a (known) bug or should I be looking for problems with my > installation? > This is by design. Release notes are the first port of call! http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/release-notes.html#removed-variable-precision-gro-writing -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] protein -ligand complex dissociating during simulation
On 7/21/17 10:56 AM, RAHUL SURESH wrote: It sounds like some internal dihedral problem. Request you, check on it. How did you deduce that? Indeed, conformational sampling may be an issue, so one should check the internal geometries of the ligands, preservation of various interactions with the protein (H-bonding and other characteristic distances and angles, etc). Revisit your parametrization, if you used some black-box method without validation and/or refinement, you may just have a junk ligand topology. -Justin On Fri, 21 Jul 2017 at 6:54 PM, Sneha Vishwanath < snehavishwanat...@gmail.com> wrote: @ Justin: I have re-imaged the trajectory with trjconv using and still the ligand dissociates from one of the chain but remain bound with the other chain. @ Gangotri: I am not sure how constraining the bond between protein might help. Can you please elaborate if possible. Thanks in advance. Sneha On Fri, Jul 21, 2017 at 6:37 PM, Justin Lemkul wrote: On 7/21/17 8:56 AM, Sneha Vishwanath wrote: Dear all I am simulating a dimeric protein, with each subunit bound to a small molecule. During the simulation, one of the ligands is dissociating from the chain and moving all around the chain while the same ligand remains bound to the chain during simulation. Experiments show that the ligand binds to both the subunit which is further supported by the experimental structure of the protein-ligand complex (which I have used for the simulation). The simulation is for 50 ns and it usually starts dissociating after 10 ns. Any thoughts on why could it be happening and how it can be circumvented? Any help would be useful. Are you sure this is not simply a PBC artifact? Have you re-imaged/centered the trajectory appropriately with trjconv? -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. -- == 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.
Re: [gmx-users] Dummy atom vs Real atom
On 7/21/17 11:30 AM, Mostafa Javaheri wrote: Dear gmx users Does anyone know how a dummy atom with no Van der Waals interactions (zero sigma and epsilon parameters) and also no mass and charges deals with other real atoms inside the simulation box? Is that possible a dummy atom with described characteristics get infinitely close to a real atom during the simulation? Or even passing through each others? "Dummy" atom may refer to a couple of different cases, but as you describe, a non-interacting species would indeed just diffuse through the box and not interact with anything (including overlap). -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.
Re: [gmx-users] Doubt about edr file after normal mode analysis
On 7/21/17 4:24 PM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I attempted to write the energy file (edr file) after performing normal mode analysis (using integrator = nm), but couldn't find gromacs writing nm.edr file at the end of the nm analysis similar to the way it writes em.edr after energy minimization. So firstly, is it plausible to write the edr file after nm analysis and if it is, what correction should I implement in the following set of gromacs commands I executed, to pull it off? grompp_d -f nmnopbc.mdp -c em.gro -p topol.top -o nm.tpr mdrun_d -v -deffnm nm -e nm.edr I don't think there is any physically meaningful energy quantity one can get from NMA, hence no .edr 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.
Re: [gmx-users] Did -ndec stop working in 2016 releases?
On 7/21/17 5:11 PM, Caro Miguel wrote: Hello, I am trying to extract trajectory data with more decimal places than the standard. I have been using gmx trjconv with the -ndec option to do this in the past. I am now using the 2016.3 release and the following command: gmx trjconv -f md.trr -s md.tpr -o traj.gro -ndec 5 gives me a traj.gro file with only 3 decimal places, which is the default. I have also tested the 2016.1 release and I experience the same problem. Gromacs 5.1.4 behaves as expected. Apparently trjconv understands -ndec since it's telling me "Setting output precision to 1e-05 (nm)", but the output .gro file is missing more decimal digits. Is this a (known) bug or should I be looking for problems with my installation? This is by design. Release notes are the first port of call! http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/release-notes.html#removed-variable-precision-gro-writing -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Did -ndec stop working in 2016 releases?
Hello, I am trying to extract trajectory data with more decimal places than the standard. I have been using gmx trjconv with the -ndec option to do this in the past. I am now using the 2016.3 release and the following command: gmx trjconv -f md.trr -s md.tpr -o traj.gro -ndec 5 gives me a traj.gro file with only 3 decimal places, which is the default. I have also tested the 2016.1 release and I experience the same problem. Gromacs 5.1.4 behaves as expected. Apparently trjconv understands -ndec since it's telling me "Setting output precision to 1e-05 (nm)", but the output .gro file is missing more decimal digits. Is this a (known) bug or should I be looking for problems with my installation? Miguel -- Dr. Miguel Caro Postdoctoral researcher Department of Electrical Engineering and Automation, and COMP Centre of Excellence in Computational Nanoscience Aalto University, Finland Email: mcar...@gmail.com Work: miguel.c...@aalto.fi Website: http://mcaroba.dyndns.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] Doubt about edr file after normal mode analysis
Dear Justin, I attempted to write the energy file (edr file) after performing normal mode analysis (using integrator = nm), but couldn't find gromacs writing nm.edr file at the end of the nm analysis similar to the way it writes em.edr after energy minimization. So firstly, is it plausible to write the edr file after nm analysis and if it is, what correction should I implement in the following set of gromacs commands I executed, to pull it off? grompp_d -f nmnopbc.mdp -c em.gro -p topol.top -o nm.tpr mdrun_d -v -deffnm nm -e nm.edr Thank you, Bhagyesh -- 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] Dummy atom vs Real atom
Dear gmx users Does anyone know how a dummy atom with no Van der Waals interactions (zero sigma and epsilon parameters) and also no mass and charges deals with other real atoms inside the simulation box? Is that possible a dummy atom with described characteristics get infinitely close to a real atom during the simulation? Or even passing through each others? Any help will be useful. Thanks M.Javaheri -- 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] protein -ligand complex dissociating during simulation
It sounds like some internal dihedral problem. Request you, check on it. On Fri, 21 Jul 2017 at 6:54 PM, Sneha Vishwanath < snehavishwanat...@gmail.com> wrote: > @ Justin: I have re-imaged the trajectory with trjconv using and still the > ligand dissociates from one of the chain but remain bound with the other > chain. > > @ Gangotri: I am not sure how constraining the bond between protein might > help. Can you please elaborate if possible. > > Thanks in advance. > > Sneha > > On Fri, Jul 21, 2017 at 6:37 PM, Justin Lemkul wrote: > > > > > > > On 7/21/17 8:56 AM, Sneha Vishwanath wrote: > > > >> Dear all > >> > >> I am simulating a dimeric protein, with each subunit bound to a small > >> molecule. During the simulation, one of the ligands is dissociating from > >> the chain and moving all around the chain while the same ligand remains > >> bound to the chain during simulation. Experiments show that the ligand > >> binds to both the subunit which is further supported by the experimental > >> structure of the protein-ligand complex (which I have used for the > >> simulation). The simulation is for 50 ns and it usually starts > >> dissociating > >> after 10 ns. > >> > >> Any thoughts on why could it be happening and how it can be > circumvented? > >> Any help would be useful. > >> > >> > > Are you sure this is not simply a PBC artifact? Have you > > re-imaged/centered the trajectory appropriately with trjconv? > > > > -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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] NEMD with sinusoidal pressure variation
Hi David, Thanks for the quick response. I am looking for a pressure wave in air with a frequency in GHz. I am looking to see the mechanical behavior of proteins. By implementing a code, do you mean implementing an external script (such as a code written in python) and then embedding it into the code for gromacs? Regards, Aarushi On Fri, Jul 21, 2017 at 3:59 AM, David van der Spoel wrote: > On 20/07/17 23:53, Aarushi Bhargava wrote: > >> I am simulating a protein using gromacs 5.0.2 and want to apply time >> varying pressure (preferably sine wave) on it. How should I do it in NEMD? >> >> You would have to code to implement a varying pressure of any sort, but > please think about what kind of physics your are trying to model first. Is > it all possible to have Ghz or even Thz pressure "waves"? If they are much > slower you have to simulate not ns or ps but much longer. > > Is the pressure coming from air or from a (glass) wall? This may affect > what you want to implement. > > Finally what measurements on proteins (just one?) will you be comparing > to? This should also influence your design decisions. > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Regarding creating a box around the molecule and neutralization of charge before EM and MD
In order to do an energy minimization and md simulation is it a must to create a box around your molecule of interest(whether it be a small or macro molecule). If so can you please explain why? -- 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] protein -ligand complex dissociating during simulation
@ Justin: I have re-imaged the trajectory with trjconv using and still the ligand dissociates from one of the chain but remain bound with the other chain. @ Gangotri: I am not sure how constraining the bond between protein might help. Can you please elaborate if possible. Thanks in advance. Sneha On Fri, Jul 21, 2017 at 6:37 PM, Justin Lemkul wrote: > > > On 7/21/17 8:56 AM, Sneha Vishwanath wrote: > >> Dear all >> >> I am simulating a dimeric protein, with each subunit bound to a small >> molecule. During the simulation, one of the ligands is dissociating from >> the chain and moving all around the chain while the same ligand remains >> bound to the chain during simulation. Experiments show that the ligand >> binds to both the subunit which is further supported by the experimental >> structure of the protein-ligand complex (which I have used for the >> simulation). The simulation is for 50 ns and it usually starts >> dissociating >> after 10 ns. >> >> Any thoughts on why could it be happening and how it can be circumvented? >> Any help would be useful. >> >> > Are you sure this is not simply a PBC artifact? Have you > re-imaged/centered the trajectory appropriately with trjconv? > > -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] protein -ligand complex dissociating during simulation
On 7/21/17 8:56 AM, Sneha Vishwanath wrote: Dear all I am simulating a dimeric protein, with each subunit bound to a small molecule. During the simulation, one of the ligands is dissociating from the chain and moving all around the chain while the same ligand remains bound to the chain during simulation. Experiments show that the ligand binds to both the subunit which is further supported by the experimental structure of the protein-ligand complex (which I have used for the simulation). The simulation is for 50 ns and it usually starts dissociating after 10 ns. Any thoughts on why could it be happening and how it can be circumvented? Any help would be useful. Are you sure this is not simply a PBC artifact? Have you re-imaged/centered the trajectory appropriately with trjconv? -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.
Re: [gmx-users] Drude force field
On 7/20/17 8:08 AM, Shraddha Parate wrote: Hi gmx users! For polarizable effect, I was setting drude force field in Gromacs I attempted running Lagrangian Dynamics simulation using Drude force field. mdp file format was used from the supporting data in below paper. [2015] Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.( http://onlinelibrary.wiley.com/doi/10.1002/jcc.23937/abstract;jsessionid=E354008D7BE6AA1A02D26C061B49163A.f02t01 ) --- ; RUN CONTROL PARAMETERS integrator = md-vv ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 1 comm-mode = linear nstcomm = 100 comm-grps = System ; OUTPUT CONTROL OPTIONS nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstcalcenergy = 100 nstenergy = 100 ; NEIGHBORSEARCHING PARAMETERS cutoff-scheme = verlet nstlist = 10 ns-type = Grid pbc = xyz rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 1.2 vdwtype = cutoff vdw-modifier = potential-switch rvdw-switch = 1.0 rvdw = 1.2 DispCorr = EnerPres ; TEMPERATURE COUPLING tcoupl = Nose-Hoover nsttcouple = 1 nh-chain-length = 1 ; Groups to couple separately tc-grps = Atoms Drues tau-t = 0.1 0.005 ref-t = 298.15 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN, OTHERWISE DO ; NOT GENERATE NEW VELOCITIES IF PREVIOUSLY EQUILIBRATED gen-vel = yes gen-temp = 298.15 gen-seed = -1 ; OPTIONS FOR BONDS constraints = none ; can also be h-bonds, not all-bonds continuation = no ; DRUDE PARAMETERS drude = yes drude-mode = Lagrangian drude-t = 1.0 drude-hardwall = yes drude-r = 0.02 drude-tsteps = 5 --- I couldn't understand [tc-grps = Atoms Drude] option. All the atoms in one group, all the Drudes in the next. If you want to break the system apart into protein and non-protein: tc-grps = Protein-Atoms Protein Drudes Non-Protein-Atoms Non-Protein-Drudes ref_t = 298.15 1.0 298.15 1.0 tau_t = 1.0 0.005 1.0 0.005 If the option is changed to [tc-grps = Protein SOL],I get a fatal error message. -- Fatal error: Incorrect thermostat setup in relative_tstat, ti = -1 -- How to resolve this issue? Why the changed parameter gives a fatal error? Do what the paper (and the ones cited therein) tell you to do. The Drude integration scheme requires a special dual thermostat that couples the Drude oscillators to a low-temperature thermostat to approximate the SCF surface. You can't treat these kinds of systems like you would additive ones. The atoms (anything non-Drude) and Drudes have to be in separate thermostats, in a given order, as explained in the paper (and shown above). Note that domain decomposition remains broken, so you can only run with OpenMP. I recently identified the (hopefully) last remaining issue but it will take some time to get it fixed as I am currently moving and starting my own lab, so my attention is elsewhere for a while. -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.
Re: [gmx-users] Ethanol energies with CHARMM ff
On 7/20/17 5:27 AM, Sonia Milena Aguilera Segura wrote: On 7/18/17 1:28 PM, Sonia Milena Aguilera Segura wrote: Dear GROMACS users, I am running a 4 nm box of ethanol and once I finished the MD, I got the right T, P, density. However, I noticed that my energies are odd. After several trials with different parameters and box sizes I >>am getting a Total Energy between -1.2 to 0.6 KJ/mol (already normalizaed, Total energy/#molecules). I checked the potential energy at the end of minimization and this was around -65 kJ/mol. Then, I >>observed that during NVT equilibration my potential energy decreased to a value around -33 kJ/mol with a kinetic energy also around the same value (33 kJ/mol), and that's why my final total energies >>and, therefore, enthalpies are giving values around 0. I ran I don't understand how you're calculating your enthalpies. The kinetic energy is irrelevant because it should cancel between the gas and liquid phases for a given temperature, so the dHvap value is /N + + RT also simulations with water, isopropanol, and acetonitrile and I am getting values of -52, -206, and-48, which seem reasonable to me. My paremeters have been already discussed in a previous mail (please see acetonitrile Reasonable based on...? -Justin Dear Justin, Currently I am not trying to calculate dHvap, only comparing the energies (Total energy/#molecules and enthalphy with -nmol and -fluct_props option for g_energy, that gives me enthalpies in kJ/mol). If I am not mistaken, in practice this enthalpy is calculated as the total energy (internal energy) plus de pV correction, all divided by the number of molecules in the system to give a value of enthalpy in kJ/mol. Is there any way to compare this energies against experimental values? For what I've understood, this value can be only comparable against a computational chemistry calculation (DFT, etc) to compare the total energy of the system. Please correct me if I am wrong. When I say that the values I am getting seem reasonable I meant that they are all non-zero values, and moreover, without really know if the value I am getting correspond to any experimental value and/or ab initio calculation, at least they are all negative and they seem to show and correspond to the strength of the molecular interactions, e.g. isopropanol displays higher energies than water and acetonitrile, which kind of correspond to strength of their molecular interactions. Moreover, the problem comes when I see the values of ethanol. No matter what, this value shouldn't be zero. Or am I missing something? Perhaps I should have started by asking the physical meaning of this values and the right approach to analyze the energies of the system. Is comparing the energies as described before a bad practice? Is computing the dHvap the only and right approach?. In this case I would also need to simulate the gas phase for my solvents, right?. However, all of them are liquid at 298. How can I simulate the gas phase at this T? The CHARMM parametrization protocol for pure liquids includes a comparison with experimental dHvap values. If you're looking to assess the integrity of the force field/your protocol, you should be looking at values that have known levels of agreement. I have no idea what to expect for just computing the enthalpy of a liquid. -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.
Re: [gmx-users] protein -ligand complex dissociating during simulation
Hey! You might want to constrain the bond between the 2 protein chains. G *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Jul 21, 2017 at 8:56 AM, Sneha Vishwanath < snehavishwanat...@gmail.com> wrote: > Dear all > > I am simulating a dimeric protein, with each subunit bound to a small > molecule. During the simulation, one of the ligands is dissociating from > the chain and moving all around the chain while the same ligand remains > bound to the chain during simulation. Experiments show that the ligand > binds to both the subunit which is further supported by the experimental > structure of the protein-ligand complex (which I have used for the > simulation). The simulation is for 50 ns and it usually starts dissociating > after 10 ns. > > Any thoughts on why could it be happening and how it can be circumvented? > Any help would be useful. > > Thanks in advance. > > Regards > Sneha Vishwanath > -- > 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] protein -ligand complex dissociating during simulation
Dear all I am simulating a dimeric protein, with each subunit bound to a small molecule. During the simulation, one of the ligands is dissociating from the chain and moving all around the chain while the same ligand remains bound to the chain during simulation. Experiments show that the ligand binds to both the subunit which is further supported by the experimental structure of the protein-ligand complex (which I have used for the simulation). The simulation is for 50 ns and it usually starts dissociating after 10 ns. Any thoughts on why could it be happening and how it can be circumvented? Any help would be useful. Thanks in advance. Regards Sneha Vishwanath -- 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] NEMD with sinusoidal pressure variation
On 20/07/17 23:53, Aarushi Bhargava wrote: I am simulating a protein using gromacs 5.0.2 and want to apply time varying pressure (preferably sine wave) on it. How should I do it in NEMD? You would have to code to implement a varying pressure of any sort, but please think about what kind of physics your are trying to model first. Is it all possible to have Ghz or even Thz pressure "waves"? If they are much slower you have to simulate not ns or ps but much longer. Is the pressure coming from air or from a (glass) wall? This may affect what you want to implement. Finally what measurements on proteins (just one?) will you be comparing to? This should also influence your design decisions. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
