Re: [gmx-users] Replica Exchange with Solute Tempering
Hi I had tried using gromacs-4.6.1 to perform solute tempering. If you go through terakawa's paper you have to describe the lambdas corresponding to the temperatures. In your topology file define the params corresponding to the two end states l=0 and l=1. Then define vdw, bonded and coulomb lambdas in the mdp file. The format is very well described in the manual. Then just the regular -replex syntax would perform solute tempering. However, the free energy module required to perform this, is extremely slow. On Oct 26, 2013 8:46 PM, David Osguthorpe david.osgutho...@gmail.com wrote: On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote: Hi, all- Rest essentially scales the solute-solvent interactions, but maintains the solute-solute interactions. This can be done solely with Hamiltonian replica exchange, which is in 4.6. It's a bit tricky, though. We plan on having something that does this automatically in 5.0 or 5.1, but it's not there yet. What do you intend to do? It could be that there's a better way to do what you want to do with Hamiltonian replica exchange, as well. Sorry - yes Im looking for an example of how to do REST via Hamiltonian replica exchange Ive seen the papers by Moors (Improved Replica Exchange Method for Native-State Protein Sampling) and Terekawa (On easy implementation of a variant of the replica exchange with solute tempering in GROMACS) and followed some of the gromacs user list discussions from 2011 on REST simulations As you say, it looks like its a bit tricky so was hoping there was a toy example somewhere Thanks David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Constraining a part of the system
Is there a way to constraint bonds of a part of the system while keeping the other part flexible? For example for a simulation with two proteins, I would like to constraint the bonds of one and would like to keep the other flexible. I would prefer to use LINCS to constraint the system -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Constraining a part of the system
@Vitaly. Yes you are right. However, I noticed that if I do not constraint the bonds in my CNT my simulations run fine. It is indeed surprising to me but I do not have much experience with simulating CNTs and if not constraining the bonds seem to get things done, I think it is a viable option. But still need to test a lot of things before I can decide on the final settings. On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Yes. That is the way to go about it. I was hoping for a more lazy approach... Thanks anyways. On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 4:50 PM, HANNIBAL LECTER wrote: Is there a smart way of writing the constraint sections in the topology file other than entering the values manually ? Write a script that parses the [bonds] directive of the post-processed topology (output by grompp -pp) and write the relevant fields to a [constraints] directive. -Justin On Tue, Sep 17, 2013 at 10:10 AM, rahul seth rahul.seth.grom...@gmail.com**wrote: Thanks On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: Is there a way to constraint bonds of a part of the system while keeping the other part flexible? For example for a simulation with two proteins, I would like to constraint the bonds of one and would like to keep the other flexible. I would prefer to use LINCS to constraint the system Set the constraints explicitly in the topology of one protein using a [constraints] directive. Then set constraints = none in the .mdp file. The constraints read from the topology will override the .mdp setting while leaving all other bonds unconstrained. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search **before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support
Re: [gmx-users] Constraining a part of the system
Yes. That is the way to go about it. I was hoping for a more lazy approach... Thanks anyways. On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 4:50 PM, HANNIBAL LECTER wrote: Is there a smart way of writing the constraint sections in the topology file other than entering the values manually ? Write a script that parses the [bonds] directive of the post-processed topology (output by grompp -pp) and write the relevant fields to a [constraints] directive. -Justin On Tue, Sep 17, 2013 at 10:10 AM, rahul seth rahul.seth.grom...@gmail.com**wrote: Thanks On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: Is there a way to constraint bonds of a part of the system while keeping the other part flexible? For example for a simulation with two proteins, I would like to constraint the bonds of one and would like to keep the other flexible. I would prefer to use LINCS to constraint the system Set the constraints explicitly in the topology of one protein using a [constraints] directive. Then set constraints = none in the .mdp file. The constraints read from the topology will override the .mdp setting while leaving all other bonds unconstrained. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search **before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Constraining a part of the system
Is there a smart way of writing the constraint sections in the topology file other than entering the values manually ? On Tue, Sep 17, 2013 at 10:10 AM, rahul seth rahul.seth.grom...@gmail.comwrote: Thanks On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: Is there a way to constraint bonds of a part of the system while keeping the other part flexible? For example for a simulation with two proteins, I would like to constraint the bonds of one and would like to keep the other flexible. I would prefer to use LINCS to constraint the system Set the constraints explicitly in the topology of one protein using a [constraints] directive. Then set constraints = none in the .mdp file. The constraints read from the topology will override the .mdp setting while leaving all other bonds unconstrained. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Constraining a part of the system
Does anyone have proper parameters for CNTs ? I have been trying to perform Simulations with finite CNTs. However, none of the parameters so far (obtained from literature) seem to give the output temperatures equal to set temperatures. I have been looked into my input files time and again, but I could not locate any bug so far. The problem is if I simulate my CNT with bonds angles dihedrals and 1-4 interactions and constraint the bonds, the temperature of the CNT seems to deviate far from the set temperature with reasonable values of tau-t using the sd integrator in GROMACS. Does anyone have parameters for CNTs such that they work with the SD integrator with reasonable tau-t values? On Tue, Sep 17, 2013 at 5:14 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: @Vitaly. Yes you are right. However, I noticed that if I do not constraint the bonds in my CNT my simulations run fine. It is indeed surprising to me but I do not have much experience with simulating CNTs and if not constraining the bonds seem to get things done, I think it is a viable option. But still need to test a lot of things before I can decide on the final settings. On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Yes. That is the way to go about it. I was hoping for a more lazy approach... Thanks anyways. On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 4:50 PM, HANNIBAL LECTER wrote: Is there a smart way of writing the constraint sections in the topology file other than entering the values manually ? Write a script that parses the [bonds] directive of the post-processed topology (output by grompp -pp) and write the relevant fields to a [constraints] directive. -Justin On Tue, Sep 17, 2013 at 10:10 AM, rahul seth rahul.seth.grom...@gmail.com**wrote: Thanks On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: Is there a way to constraint bonds of a part of the system while keeping the other part flexible? For example for a simulation with two proteins, I would like to constraint the bonds of one and would like to keep the other flexible. I would prefer to use LINCS to constraint the system Set the constraints explicitly in the topology of one protein using a [constraints] directive. Then set constraints = none in the .mdp file. The constraints read from the topology will override the .mdp setting while leaving all other bonds unconstrained. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search **before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx
Re: Fwd: [gmx-users] SD integrator
Thanks. From your publications it seems that you have been simulating with infinite CNTs. I am trying to use finite CNTs and I am generating my topology files according to http://chembytes.wikidot.com/grocnt. I am modeling the peripheral Carbon atoms with two bonds by specifying it in the atomname2type.n2t file. I am still not sure as to what is the source of this discrepancy. After a few tests I think this can be caused by improper parameterization of the bonds but I am not sure how to go about correcting any discrepancies. On Fri, Sep 13, 2013 at 5:53 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Do you couple CNT as a separate T-group? It should be done so. I think your systems blows up because of incorrectly defined bonded parameters for the tube, not due to thermostatting. For instance, you might not define all the valence angles and dihedrals. See my papers for the parameters for CNT, if you need such... Dr. Vitaly V. Chaban On Fri, Sep 13, 2013 at 8:55 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: However, even if position restraints are not used, the error can be reproduced. I am constraining the bonds in my CNTs though. I was wondering if you could point me to some parameters for CNT. On Fri, Sep 13, 2013 at 1:50 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: I am position restraining the CNT group. That affects the degrees of freedom. On Sep 13, 2013 1:43 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: There must be some problem with degrees of freedom in your system... Dr. Vitaly V. Chaban -- Forwarded message -- From: HANNIBAL LECTER hanniballecte...@gmail.com Date: Fri, Sep 13, 2013 at 7:15 PM Subject: [gmx-users] SD integrator To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all, I have been posting for a while with my problems in simulating peptides inside CNTs. After a lot of trials it seems like simulating the CNT with bonds and angles seems like a wise thing to do. I am using the SD integrator + PR barostat. It seems like improper thermostatting can blow up the system. For example, when I am trying to simulate with tau-t for CNT as 1.0 the system blows up for 300K. The output temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K. However, if a stronger coupling is used tau-t = 0.005, the system works fine. Are there any artifacts for coupling the CNT group with such a low tau-t? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] SD integrator
Hi all, I have been posting for a while with my problems in simulating peptides inside CNTs. After a lot of trials it seems like simulating the CNT with bonds and angles seems like a wise thing to do. I am using the SD integrator + PR barostat. It seems like improper thermostatting can blow up the system. For example, when I am trying to simulate with tau-t for CNT as 1.0 the system blows up for 300K. The output temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K. However, if a stronger coupling is used tau-t = 0.005, the system works fine. Are there any artifacts for coupling the CNT group with such a low tau-t? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Quick question about pressure coupling
I am trying to simulate a peptide inside a nanotube and using isotropic pressure coupling for the system. The nanotube is immersed in a cuboidal box of water and aligned along the z direction of the box. The XX, YY components of the stress tensor are about ~570 bars and the ZZ component is about -1179 yielding a total pressure of about 2 bars whereas my set pressure is ~1.01325 bars. Is this okay or should I be using semiisotropic coupling? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Quick question about pressure coupling
500ps simulations. Yes everything is immersed in a bath of water. Can you please elaborate a little more as to why do you doubt semiisotropic coupling may not be necessary? On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:01 AM, HANNIBAL LECTER wrote: I am trying to simulate a peptide inside a nanotube and using isotropic pressure coupling for the system. The nanotube is immersed in a cuboidal box of water and aligned along the z direction of the box. The XX, YY components of the stress tensor are about ~570 bars and the ZZ component is about -1179 yielding a total pressure of about 2 bars whereas my set pressure is ~1.01325 bars. Is this okay or should I be using semiisotropic coupling? Over how long a time period are these values? If everything is immersed in a bath of water, I doubt semiisotropic coupling is necessary. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Quick question about pressure coupling
Yes On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:09 AM, HANNIBAL LECTER wrote: 500ps simulations. Yes everything is immersed in a bath of water. Can you please elaborate a little more as to why do you doubt semiisotropic coupling may not be necessary? Water should compress isotropically. I understand where you're coming from, given that you have observed a seemingly semiisotropic compression of the system, but physically that is not right. Something like a membrane, that has properties that make it sensible to couple x-y and z compression separately, would use semiisotropic coupling. Is this a system in which you're using freezegrps? -Justin On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:01 AM, HANNIBAL LECTER wrote: I am trying to simulate a peptide inside a nanotube and using isotropic pressure coupling for the system. The nanotube is immersed in a cuboidal box of water and aligned along the z direction of the box. The XX, YY components of the stress tensor are about ~570 bars and the ZZ component is about -1179 yielding a total pressure of about 2 bars whereas my set pressure is ~1.01325 bars. Is this okay or should I be using semiisotropic coupling? Over how long a time period are these values? If everything is immersed in a bath of water, I doubt semiisotropic coupling is necessary. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Quick question about pressure coupling
Would there be artifacts because of that? On Wed, Sep 11, 2013 at 9:20 AM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Yes On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:09 AM, HANNIBAL LECTER wrote: 500ps simulations. Yes everything is immersed in a bath of water. Can you please elaborate a little more as to why do you doubt semiisotropic coupling may not be necessary? Water should compress isotropically. I understand where you're coming from, given that you have observed a seemingly semiisotropic compression of the system, but physically that is not right. Something like a membrane, that has properties that make it sensible to couple x-y and z compression separately, would use semiisotropic coupling. Is this a system in which you're using freezegrps? -Justin On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:01 AM, HANNIBAL LECTER wrote: I am trying to simulate a peptide inside a nanotube and using isotropic pressure coupling for the system. The nanotube is immersed in a cuboidal box of water and aligned along the z direction of the box. The XX, YY components of the stress tensor are about ~570 bars and the ZZ component is about -1179 yielding a total pressure of about 2 bars whereas my set pressure is ~1.01325 bars. Is this okay or should I be using semiisotropic coupling? Over how long a time period are these values? If everything is immersed in a bath of water, I doubt semiisotropic coupling is necessary. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Freeze + NPT + constraints
Hi, Sorry to bother you again regarding this. But I am not sure, as to why freeze + constraints should not work during a NPT simulation? The update algorithm as shown in the manual does not say anything that would fundamentally prevent this. In fact, one can use freezegroups + constraints in NVT. What prevents it from running in NPT? I get the foll. error. step 0 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. ... ... ... Segmentation fault -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freeze + NPT + constraints
I would think that too. However, that is not what happens. If you freeze a group it gets scaled according to the box vectors during a npt simulation. Hence in order to keep the group (in my case a carbon nano tube) of fixed diameter i use position restraints. This protocol works fine with with npt simulations. Now, i wanted to check if i include the bonded interactions in my topology and constrain all the bonds things should not matter at all, since the bonded interactions are redundant in this case. However, that is not the case and the system crashes. If however the bonds are not constrained, things work fine. I know this is a very round about way of getting things done, still i am curious. On Sep 10, 2013 4:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 2:59 PM, HANNIBAL LECTER wrote: Hi, Sorry to bother you again regarding this. But I am not sure, as to why freeze + constraints should not work during a NPT simulation? The update algorithm as shown in the manual does not say anything that would fundamentally prevent this. In fact, one can use freezegroups + constraints in NVT. What prevents it from running in NPT? The use of a barostat requires that the positions of the atoms can be scaled according to the pressure. Freezing atoms, by definition, makes them immobile and thus they cannot be scaled. Thus, the two algorithms are fundamentally incompatible. -Justin I get the foll. error. step 0 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. ... ... ... Segmentation fault -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Documentation for the variables used in gromacs sourcecode
Hi, I was wondering if there is a documentation of all the source code variables is available or not. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs 4.6.3 Installation Issues,
probably u do not have CUDA. If you are not really interested in performing simulations using GPU, you can set -DGMX_GPU=off during cmake On Sat, Aug 24, 2013 at 12:15 PM, No One not1morepara...@yahoo.com wrote: hi, i'm having difficulties installing gromacs by creating static links to the libraries for fftw3. i am currently running: cygwin1.7.24-1 cmake2.8.11.2-1 fftw33.3.3-1 this is the input that i'm attempting to utilize and flags errors (and some combination there of): cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs this is my error output: /cygdrive/c/gromacs/gromacs-4.6.3/build-cmake $ cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs .. -- Could NOT find CUDA (missing: CUDA_CUDART_LIBRARY) (found suitable version 5.5, minimum required is 3.2) -- Enabling native GPU acceleration CMake Error at cmake/FindFFTW.cmake:122 (message): The FFTW library /usr/local/lib/libfftw3f.a cannot be used with shared libraries. Provide a different FFTW library by setting FFTWF_LIBRARY. If you don't have a different one, recompile FFTW with --enable-shared or --with-pic. Or disable shared libraries for Gromacs by setting BUILD_SHARED_LIBS to no. Note: Disabling shared libraries requires up to 10x as much disk space. Call Stack (most recent call first): CMakeLists.txt:948 (find_package) any assistance would be appreciated. thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT, freezegroups and Position Restraints.
Thanks a lot. I could set up and perform the simulations using position restraints and md+nose-hoover thermostat as suggested by Justin. The combination seems to yield the correct canonical ensembles. Equilibration with Berendsen barostat (with integrator=sd and refcoord-scaling = com) does not seem to have any problems. However, while performing simulations with parrinello-rahman barostat and refcoord-scaling=com using either sd or md, my system blows up. However, refcoord-scaling=all does not seem to have any issues. My position restraints are applied only to the CNT atoms and I am trying to simulate peptide near CNTs. All bonds are constrained in my simulations. Is there anything I am overlooking while moving from refcoord-scaling=com to refcoord-scaling=all? On Thu, Aug 22, 2013 at 6:20 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Thu, Aug 22, 2013 at 12:51 AM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Thanks. I am not interested in the real physics of the freezegroups as I am assuming the fluctuations are negligible in the timescale of the fluctuations of the non-freeze groups. That may be true in the case where the non-interesting group is unfrozen, but it does not follow that the perturbation to the Hamiltonian from freezing the atoms (ie. that all interactions with them now don't follow Newton's third law) is equally negligible. I thought that the langevin thermostat is quite effective in this case just to ensure that there is no net heat flow from the hot to the cold freeze groups. I maybe missing something. There's no heat flow at all to the frozen groups because they have no velocity, so no temperature and no coupling. The atoms near the frozen groups are going to be weird, and that has flow-on effects. Whether those effects are significant is up to you to show, but you should have a much easier time setting up a stable non-frozen CNT. Freezing a group does not make your simulation appreciably faster. If I were to review a paper that used freeze groups and made no attempt to show the results were unaffected, then that paper would be on the fast track for rejection... Relying on the thermostat to mask errors in the model physics or the integration of it is similarly reprehensible, IMO. :-) Mark On Wed, Aug 21, 2013 at 6:03 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: I am not sure what is the problem with using NPT, constraints and freezegroups. Unless there is some fundamental issue (which I cannot think of) one should in principle be able to run NPT with the CNT system by freezing the CNT group. Frozen atoms do not have velocity, and the energy they would have acquired in the update step is simply removed. So you get a discontinuity every time step, because the new configuration did not evolve from the previous one in a way that could mimic the statistics of the ensemble with no frozen atoms. Also, there must be net flow of heat if the temperature is constant in (even just) NVT, so you're not modelling a normal ensemble at all. Constraints and box-size rescaling in NPT make things worse. I can't imagine a use case (other than equilibration of a problematic system) where you could use freeze groups and believe you were modelling something like real physics. I am using sd with LINCS to constraint the bonds. However, if md is used with SHAKE the system crashes with segmentation fault. Does anyone have any idea as to what could be the problem? Using freeze groups. Mark On Mon, Aug 19, 2013 at 6:40 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Interestingly, removing position restraints does not have much of an impact. On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. What about changing the integrator to md? What happens if you remove restraints while using sd? -Justin On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The refcoord-scaling option doesn't matter with frozen groups. Anything that is frozen, by definition, never has its position updated. Under the influence of pressure coupling, other particles around the frozen group can have their positions scaled and thus collide with the frozen group, which has remained in its original location. The outputs
Re: [gmx-users] NPT, freezegroups and Position Restraints.
I am not sure what is the problem with using NPT, constraints and freezegroups. Unless there is some fundamental issue (which I cannot think of) one should in principle be able to run NPT with the CNT system by freezing the CNT group. I am using sd with LINCS to constraint the bonds. However, if md is used with SHAKE the system crashes with segmentation fault. Does anyone have any idea as to what could be the problem? On Mon, Aug 19, 2013 at 6:40 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Interestingly, removing position restraints does not have much of an impact. On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. What about changing the integrator to md? What happens if you remove restraints while using sd? -Justin On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The refcoord-scaling option doesn't matter with frozen groups. Anything that is frozen, by definition, never has its position updated. Under the influence of pressure coupling, other particles around the frozen group can have their positions scaled and thus collide with the frozen group, which has remained in its original location. The outputs are from g_energy. OK, good. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc = xyz integrator = sd ld_seed = 215546 dt = 0.002; ps ! nsteps = 5; 50 ns ;nsteps = 125000; 250 ps nstcomm = 10 nstcalcenergy = 10 nstxout = 0 nstxtcout = 5000 ;every 10 ps nstvout = 100 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off rvdw= 1.0 coulombtype = pme rcoulomb= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tc-grps = Protein CNT SOL tau_t = 1.0 1.0 1.0 Note that tau_t is the inverse friction constant, not the normal coupling constant. In this case, I don't know what appropriate values are, especially if one of your groups is restrained. The manual advises a value of 2.0, so at least try that. Otherwise, try coupling the System as a whole or use a different integrator (i.e., md) to try to figure out the origin of the problem. -Justin ref_t = 300.000 300 300 ;freezegrps = CNT ;freezedim = Y Y Y ; Energy monitoring energygrps = CNT Protein SOL ; energygrp-excl = CNT CNT ; Isotropic pressure coupling is now on Pcoupl = Berendsen refcoord-scaling= com Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.000 gen_seed=981487 On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. That is to be expected. Frozen atoms and pressure coupling are fundamentally incompatible. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein, CNT and SOL separately, the temperature of the peptide is lower than 300K (~395K) while the temperature of the CNT is 157K. The target temperature is 300K in all cases. Can any please explain why such discrepancies are occurring? Are these temperatures from g_energy or g_traj? Can you please post a full .mdp file? -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http
Re: [gmx-users] NPT, freezegroups and Position Restraints.
Thanks. I am not interested in the real physics of the freezegroups as I am assuming the fluctuations are negligible in the timescale of the fluctuations of the non-freeze groups. I thought that the langevin thermostat is quite effective in this case just to ensure that there is no net heat flow from the hot to the cold freeze groups. I maybe missing something. On Wed, Aug 21, 2013 at 6:03 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: I am not sure what is the problem with using NPT, constraints and freezegroups. Unless there is some fundamental issue (which I cannot think of) one should in principle be able to run NPT with the CNT system by freezing the CNT group. Frozen atoms do not have velocity, and the energy they would have acquired in the update step is simply removed. So you get a discontinuity every time step, because the new configuration did not evolve from the previous one in a way that could mimic the statistics of the ensemble with no frozen atoms. Also, there must be net flow of heat if the temperature is constant in (even just) NVT, so you're not modelling a normal ensemble at all. Constraints and box-size rescaling in NPT make things worse. I can't imagine a use case (other than equilibration of a problematic system) where you could use freeze groups and believe you were modelling something like real physics. I am using sd with LINCS to constraint the bonds. However, if md is used with SHAKE the system crashes with segmentation fault. Does anyone have any idea as to what could be the problem? Using freeze groups. Mark On Mon, Aug 19, 2013 at 6:40 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Interestingly, removing position restraints does not have much of an impact. On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. What about changing the integrator to md? What happens if you remove restraints while using sd? -Justin On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The refcoord-scaling option doesn't matter with frozen groups. Anything that is frozen, by definition, never has its position updated. Under the influence of pressure coupling, other particles around the frozen group can have their positions scaled and thus collide with the frozen group, which has remained in its original location. The outputs are from g_energy. OK, good. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc = xyz integrator = sd ld_seed = 215546 dt = 0.002; ps ! nsteps = 5; 50 ns ;nsteps = 125000; 250 ps nstcomm = 10 nstcalcenergy = 10 nstxout = 0 nstxtcout = 5000 ;every 10 ps nstvout = 100 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off rvdw= 1.0 coulombtype = pme rcoulomb= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tc-grps = Protein CNT SOL tau_t = 1.0 1.0 1.0 Note that tau_t is the inverse friction constant, not the normal coupling constant. In this case, I don't know what appropriate values are, especially if one of your groups is restrained. The manual advises a value of 2.0, so at least try that. Otherwise, try coupling the System as a whole or use a different integrator (i.e., md) to try to figure out the origin of the problem. -Justin ref_t = 300.000 300 300 ;freezegrps = CNT ;freezedim = Y Y Y ; Energy monitoring energygrps = CNT Protein SOL ; energygrp-excl = CNT CNT ; Isotropic pressure coupling is now on Pcoupl = Berendsen refcoord-scaling= com Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.000 gen_seed=981487 On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul jalem...@vt.edu wrote
[gmx-users] NPT, freezegroups and Position Restraints.
Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein, CNT and SOL separately, the temperature of the peptide is lower than 300K (~395K) while the temperature of the CNT is 157K. The target temperature is 300K in all cases. Can any please explain why such discrepancies are occurring? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT, freezegroups and Position Restraints.
Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The outputs are from g_energy. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc = xyz integrator = sd ld_seed = 215546 dt = 0.002; ps ! nsteps = 5; 50 ns ;nsteps = 125000; 250 ps nstcomm = 10 nstcalcenergy = 10 nstxout = 0 nstxtcout = 5000 ;every 10 ps nstvout = 100 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off rvdw= 1.0 coulombtype = pme rcoulomb= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tc-grps = Protein CNT SOL tau_t = 1.0 1.0 1.0 ref_t = 300.000 300 300 ;freezegrps = CNT ;freezedim = Y Y Y ; Energy monitoring energygrps = CNT Protein SOL ; energygrp-excl = CNT CNT ; Isotropic pressure coupling is now on Pcoupl = Berendsen refcoord-scaling= com Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.000 gen_seed=981487 On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. That is to be expected. Frozen atoms and pressure coupling are fundamentally incompatible. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein, CNT and SOL separately, the temperature of the peptide is lower than 300K (~395K) while the temperature of the CNT is 157K. The target temperature is 300K in all cases. Can any please explain why such discrepancies are occurring? Are these temperatures from g_energy or g_traj? Can you please post a full .mdp file? -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT, freezegroups and Position Restraints.
I am performing NPT here but this artifact is independent of whether one is using NPT or NVT. On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The outputs are from g_energy. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc = xyz integrator = sd ld_seed = 215546 dt = 0.002; ps ! nsteps = 5; 50 ns ;nsteps = 125000; 250 ps nstcomm = 10 nstcalcenergy = 10 nstxout = 0 nstxtcout = 5000 ;every 10 ps nstvout = 100 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off rvdw= 1.0 coulombtype = pme rcoulomb= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tc-grps = Protein CNT SOL tau_t = 1.0 1.0 1.0 ref_t = 300.000 300 300 ;freezegrps = CNT ;freezedim = Y Y Y ; Energy monitoring energygrps = CNT Protein SOL ; energygrp-excl = CNT CNT ; Isotropic pressure coupling is now on Pcoupl = Berendsen refcoord-scaling= com Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.000 gen_seed=981487 On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. That is to be expected. Frozen atoms and pressure coupling are fundamentally incompatible. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein, CNT and SOL separately, the temperature of the peptide is lower than 300K (~395K) while the temperature of the CNT is 157K. The target temperature is 300K in all cases. Can any please explain why such discrepancies are occurring? Are these temperatures from g_energy or g_traj? Can you please post a full .mdp file? -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT, freezegroups and Position Restraints.
I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The refcoord-scaling option doesn't matter with frozen groups. Anything that is frozen, by definition, never has its position updated. Under the influence of pressure coupling, other particles around the frozen group can have their positions scaled and thus collide with the frozen group, which has remained in its original location. The outputs are from g_energy. OK, good. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc = xyz integrator = sd ld_seed = 215546 dt = 0.002; ps ! nsteps = 5; 50 ns ;nsteps = 125000; 250 ps nstcomm = 10 nstcalcenergy = 10 nstxout = 0 nstxtcout = 5000 ;every 10 ps nstvout = 100 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off rvdw= 1.0 coulombtype = pme rcoulomb= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tc-grps = Protein CNT SOL tau_t = 1.0 1.0 1.0 Note that tau_t is the inverse friction constant, not the normal coupling constant. In this case, I don't know what appropriate values are, especially if one of your groups is restrained. The manual advises a value of 2.0, so at least try that. Otherwise, try coupling the System as a whole or use a different integrator (i.e., md) to try to figure out the origin of the problem. -Justin ref_t = 300.000 300 300 ;freezegrps = CNT ;freezedim = Y Y Y ; Energy monitoring energygrps = CNT Protein SOL ; energygrp-excl = CNT CNT ; Isotropic pressure coupling is now on Pcoupl = Berendsen refcoord-scaling= com Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.000 gen_seed=981487 On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. That is to be expected. Frozen atoms and pressure coupling are fundamentally incompatible. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein, CNT and SOL separately, the temperature of the peptide is lower than 300K (~395K) while the temperature of the CNT is 157K. The target temperature is 300K in all cases. Can any please explain why such discrepancies are occurring? Are these temperatures from g_energy or g_traj? Can you please post a full .mdp file? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences
Re: [gmx-users] NPT, freezegroups and Position Restraints.
Interestingly, removing position restraints does not have much of an impact. On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. What about changing the integrator to md? What happens if you remove restraints while using sd? -Justin On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The refcoord-scaling option doesn't matter with frozen groups. Anything that is frozen, by definition, never has its position updated. Under the influence of pressure coupling, other particles around the frozen group can have their positions scaled and thus collide with the frozen group, which has remained in its original location. The outputs are from g_energy. OK, good. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc = xyz integrator = sd ld_seed = 215546 dt = 0.002; ps ! nsteps = 5; 50 ns ;nsteps = 125000; 250 ps nstcomm = 10 nstcalcenergy = 10 nstxout = 0 nstxtcout = 5000 ;every 10 ps nstvout = 100 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off rvdw= 1.0 coulombtype = pme rcoulomb= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tc-grps = Protein CNT SOL tau_t = 1.0 1.0 1.0 Note that tau_t is the inverse friction constant, not the normal coupling constant. In this case, I don't know what appropriate values are, especially if one of your groups is restrained. The manual advises a value of 2.0, so at least try that. Otherwise, try coupling the System as a whole or use a different integrator (i.e., md) to try to figure out the origin of the problem. -Justin ref_t = 300.000 300 300 ;freezegrps = CNT ;freezedim = Y Y Y ; Energy monitoring energygrps = CNT Protein SOL ; energygrp-excl = CNT CNT ; Isotropic pressure coupling is now on Pcoupl = Berendsen refcoord-scaling= com Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.000 gen_seed=981487 On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. That is to be expected. Frozen atoms and pressure coupling are fundamentally incompatible. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein, CNT and SOL separately, the temperature of the peptide is lower than 300K (~395K) while the temperature of the CNT is 157K. The target temperature is 300K in all cases. Can any please explain why such discrepancies are occurring? Are these temperatures from g_energy or g_traj? Can you please post a full .mdp file? -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists
[gmx-users] Regarding TCoupling and position restraints
Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding TCoupling and position restraints
Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? Constraints are restraints are different. If you are using constraints on any bonds in your system, the value from g_traj is wrong and you have to manually correct for it. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] extraction of PDB from clusters.pdb
You can do it by using simple shell scripting On Jul 17, 2013 12:58 AM, Shine A shin...@iisertvm.ac.in wrote: Sir, Using g_cluster I clustered snapshots in md trajectory using the command as follows g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -dt 10 Here I got clusters.pdb having central structures in each cluster. Is there any command line option available to extract all individual files from clusters.pdb. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Extending Simulations
It is not very clear as to what you are trying to do? If you have the final coordinates and velocities from a previous simulation, I would recommend start a simulation using the .gro file and ensuring that you have gen-vel=no in the .mdp file. If you have a well-equilibrated system, then the properties should not vary much. On similar lines, you can stitch multiple .edr files using eneconv. On Wed, Jun 26, 2013 at 3:54 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I have a question that relates to reproducibility in Gromacs. If I have a .cpt file from a previous simulation and use that for two simulations using tpbconv, how similar should the temperature graphs etc be? When I use the .edr files to plot various properties, there is significant difference between the two graphs and I am not sure how much is acceptable or expected. Along the same lines, is there any way to get exactly (or as close as possible) same trajectories etc that I am missing out on? I am passing the .cpt file to mdrun but are there other niggling details I should take into consideration? Thank you! -- View this message in context: http://gromacs.5086.x6.nabble.com/Extending-Simulations-tp5009399.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Membrane Equilibration
ref_p= 0.0 0.0 ?? Are you sure about this?? On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: what happens to your energy before the observed crash? does the crash happen at the same time-step each time? Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 5:22 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman coupling. However, I read that Parinello-Rahman is not great for equilibration so I thought I would do a small run using the Berendsen barostat to decrease the chances of large oscillations. I then used the .gro file obtained from that run to start a new run using Parrinello-Rahman. I am not sure if that's the correct way to go about doing what I want to do. My Parrinello run also terminated a little while in, with the error that 2 of my atoms have moved further apart than the cut-off distance. A part of my mdp file is pasted below and I was wondering if anyone had any suggestions as to stop that from happening. My time step is 0.02 ps and I thought increasing tau-p might work. I am using the compressibility from the map file on the Martini website and am worried that might be too large. Any help will be super useful! Let me know if you need any more information. ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = nose-hoover ; Groups to couple separately = tc-grps = DPPC W ; Time constant (ps) and reference temperature (K) = tau_t= 1.0 1.0 ref_t= 320 320 nsttcouple = 1 ; Pressure coupling = Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 5.0 5.0 compressibility = 3e-4 3e-4 ref_p= 0.0 0.0 nstpcouple = 5 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 105 gen_seed = 473529 -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Free Energy Calculations in Gromacs
Thank you Professor Shirts. So now my protein itp file looks like this: [ atoms ] ; nrtype resnr residue atom cgnr chargemasstypeB chargeB MassB 1 CT1ACECH3 1 -0.190264 12.01 CT_per -0.12033412.01 [ bonds ] ;ai aj func th0 kb th0B kbB 1 2 1 0.10900 284512.0 0.10900113804.8 [ pairs ] 1 8 1 [ angles ] ;ai ajak funct th0 kb th0B kbB 2 1 3 1 109.500 292.880 109.500117.152 . [ dihedrals ] ij kl func th0 cth mult th0B cthB multB 2 1 5 6 9180.0 2.86144 1180.01.14458 1 Now, I have created 6 different lambda values and placed a well-equilibrated structure and the same topology file (with values corresp. to lambda=0 and lambda =1) within six directories. The .mdp files contain the information (init-lambda-state=0,1,..) which lambda state is it. Is my approach correct ? Secondly, when I grompp followed by gmxdump -s *.tpr I find, that there is no difference in hamiltonian between the two. So, does the scaling take place during runtime? Third, since in state B only the hamiltonian is rescaled (the perturbed entries are defined in ffnonbonded.itp file) do I need to explicitly add another section [ pairs_nb ]? Again, I thank you for replying. On Sat, Apr 20, 2013 at 5:52 PM, Michael Shirts mrshi...@gmail.com wrote: You have to change atom types. For example: [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon h1h1 0. 0. A 2.47135e-01 6.56888e-02 h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02 ; perturbed The mass and charge can be zero, because they will be defined in the [ atoms ] part [ atoms ] ; nrtype resnr residue atom cgnr chargemasstypeB chargeB MassB 1 h1 1 BLAHH1a 1 -0.0891.008h1_pert -0.030 1.008; perturbed On Sat, Apr 20, 2013 at 4:04 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values. In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of the similar terms of State A. It's not quite clear to me (going through the archives of the gmx-users mailing list how to perform these calculations. One way to do this, is to use a single topology file in which the charges and the other terms are specified for both states A and B. However, it is not clear as to how should I scale the epsilons in the topology file. (My atoms are not mutated in state B. They are the same atoms with scaled epsilons.) Secondly, since I have the topology files for states A and B, is there a way I could perform the simulations (any particular way in grompp) where both the topology files can be preprocessed designating the end states and using the mdp options, the simulations corresponding to the intermediate lambda values performed?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Free Energy Calculations in Gromacs
Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values. In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of the similar terms of State A. It's not quite clear to me (going through the archives of the gmx-users mailing list how to perform these calculations. One way to do this, is to use a single topology file in which the charges and the other terms are specified for both states A and B. However, it is not clear as to how should I scale the epsilons in the topology file. (My atoms are not mutated in state B. They are the same atoms with scaled epsilons.) Secondly, since I have the topology files for states A and B, is there a way I could perform the simulations (any particular way in grompp) where both the topology files can be preprocessed designating the end states and using the mdp options, the simulations corresponding to the intermediate lambda values performed?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
