[gmx-users] PBC correction to visualize a protein-membrane structure
Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I still get the same structure. Even more weird is that when I turn on the periodic images option in vmd I still don’t see the right protein embedded into the lipid bilayer. As this can’t be a real effect of minimisation, I'd like to ask for your advice. Thank you. Juan C. Munoz-Garcia [cid:4B5D112B-EF13-4ACA-8368-671C6FE699A8] -- 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] PBC correction to visualize a protein-membrane structure
Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I still get the same structure. Even more weird is that when I turn on the periodic images option in vmd I still don’t see the right protein embedded into the lipid bilayer. As this can’t be a real effect of minimisation, I'd like to ask you for advice. Thank you. Juan C. Munoz-Garcia [cid:37CD9EEE-6F74-43E1-A009-4D0D487104FD] -- 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] PBC correction to visualize a protein-membrane structure
On 5/16/14, 4:04 AM, Juan Munoz-Garcia wrote: Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I still get the same structure. Even more weird is that when I turn on the periodic images option in vmd I still don’t see the right protein embedded into the lipid bilayer. As this can’t be a real effect of minimisation, I'd like to ask for your advice. The mailing list does not accept attachments. Please post links to images or files to download. An exact sequence of commands would be useful, as well. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] PBC correction to visualize a protein-membrane structure
Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png Thank you. Regards. Juan C. -- 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] PBC correction to visualize a protein-membrane structure
On 5/16/14, 9:08 AM, Juan Munoz-Garcia wrote: Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png Your system was probably centered at z=0 instead of z = z_box/2 (commands used for building the system would also help - I guess I should have been more clear), hence it's getting split across PBC. trjconv -trans in conjunction with -pbc mol should be what you need. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] berendsen vs parrinello-rahman
Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Thanks Nilesh -- 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] Degree of hydrogen bonding
Hi Abraham, When I do the indexing, the hbndx gives all h-bonds in ascending order for all frames and i see the a lot of repeated bonding with the same acceptor atom. Is it possible to get the index for a particular frame? I see the option -dt but i didn't quite get that one. Also, the hbnum.xvg file, the second column represent hydrogen bonds and the third column represents the pairs within 0.35nm. what does pair represent over here? Does it mean two h-bonds or donor acceptor number? Thank you, On Thu, May 8, 2014 at 4:24 PM, Udaya Dahal dahal.ud...@gmail.com wrote: Thank you. On Thu, May 8, 2014 at 12:49 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Hi, Check out g_hbond -h... documentation is written for a reason ;-) You sound like you want to see the existence matrix. You might want to create some index groups for small parts of your polymer, unless you want to drown while interpreting -hbn and -hbm. Mark On Thu, May 8, 2014 at 5:21 PM, Udaya Dahal dahal.ud...@gmail.com wrote: Thank you Justin for quick reply. I did exactly what you have mentioned but the thing is I am getting number of hydrogen bonds per monomer higher than what i was expecting. Is it possible to see which polymer atom have the hydrogen bond.( I mean is there a way to see specific atoms using the indexing so that I can compare the visual image to that number. On Tue, May 6, 2014 at 10:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/14, 6:05 PM, Udaya Dahal wrote: Hi all, I am simulating a PPO chain in water. I am looking for the degree of hydration. Currently, I am using n=27 monomer CH3-(O-CH(CH3)-CH2)n -O-CH3. I have total 4046 water molecules in a box of 5 5 5. When I use the g_hbond it says it gives the hydrogen bond and the pairs in (0.35nm) distance. As it seems it gives the total hydrogen bonds in the system. I am wondering if there is a way to calculate the total numbers of h-bond between the polymer and the water. Yes, if you select your polymer and water as the two groups for analysis, this is precisely what you should get. If you select the whole system, you'll likely get some ridiculously high number. Since I am not familiar with the programming language( reading the huge code is out of question for the time being). The model is the atomistic one and and the water i am using is spce. Also how do the boundary bonds are calculated since for a small box, the omission of the boundary bonds will completely alter the property. Nearly all Gromacs tools deal with PBC elegantly. g_hbond works fine with PBC. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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. -- Udaya Dahal, Graduate Assistant, Department of Physics, University of Connecticut -- 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. -- Udaya Dahal, Graduate Assistant, Department of Physics, University of Connecticut -- Udaya Dahal, Graduate Assistant, Department of Physics, University of Connecticut -- 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] berendsen vs parrinello-rahman
On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Is there any prior equilibration? Using P-R for the initial phase of equilibration can be unstable. 4.0.7 was a bit more forgiving, and this same issue has been reported several times before with the 4.5.x series, with the solution being to set nstpcouple = 1 for the initial phase of equilibration with P-R. I did the simulations for two different initial structure. 1. Pre-equilibrated 2. New initial structure. Nilesh -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] PBC correction to visualize a protein-membrane structure
Dear Justin, thank you. I’ve tried the following but neither of them worked, I get the same result. trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc mol -ur compact This is the last line of my input.gro file 19.51671 19.51671 13.80040 0.0 0.0 0.0 0.0 9.75836 9.75836 Juan C. Your system was probably centered at z=0 instead of z = z_box/2 (commands used for building the system would also help - I guess I should have been more clear), hence it's getting split across PBC. trjconv -trans in conjunction with -pbc mol should be what you need. -Justin -- Begin forwarded message: From: Juan Carlos Munoz Garcia juan.munoz-gar...@bioch.ox.ac.ukmailto:juan.munoz-gar...@bioch.ox.ac.uk Subject: Re: PBC correction to visualize a protein-membrane structure Date: 16 May 2014 14:08:50 BST To: gromacs.org_gmx-users@maillist.sys.kth.semailto:gromacs.org_gmx-users@maillist.sys.kth.se Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png Thank you. Regards. Juan C. -- 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] PBC correction to visualize a protein-membrane structure
On May 16, 2014 7:03 PM, Juan Munoz-Garcia juan.munoz-gar...@bioch.ox.ac.uk wrote: Dear Justin, thank you. I’ve tried the following but neither of them worked, I get the same result. trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc mol -ur compact You need to use numbers. Mark This is the last line of my input.gro file 19.51671 19.51671 13.80040 0.0 0.0 0.0 0.0 9.75836 9.75836 Juan C. Your system was probably centered at z=0 instead of z = z_box/2 (commands used for building the system would also help - I guess I should have been more clear), hence it's getting split across PBC. trjconv -trans in conjunction with -pbc mol should be what you need. -Justin -- Begin forwarded message: From: Juan Carlos Munoz Garcia juan.munoz-gar...@bioch.ox.ac.ukmailto: juan.munoz-gar...@bioch.ox.ac.uk Subject: Re: PBC correction to visualize a protein-membrane structure Date: 16 May 2014 14:08:50 BST To: gromacs.org_gmx-users@maillist.sys.kth.semailto: gromacs.org_gmx-users@maillist.sys.kth.se Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png Thank you. Regards. Juan C. -- 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] berendsen vs parrinello-rahman
Unstable models or unstable initial conditions will behave unpredictably. Unfortunately you've not given us much to go on. Mark On May 16, 2014 6:08 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Is there any prior equilibration? Using P-R for the initial phase of equilibration can be unstable. 4.0.7 was a bit more forgiving, and this same issue has been reported several times before with the 4.5.x series, with the solution being to set nstpcouple = 1 for the initial phase of equilibration with P-R. I did the simulations for two different initial structure. 1. Pre-equilibrated 2. New initial structure. Nilesh -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] berendsen vs parrinello-rahman
One initial structure is equilibrated for 10ns using Gromacs VERSION 4.0.7. If I run same structure with same .mdp and same force field parameters using gromacs VERSION 4.5.5. I got the error system is blowing up. I made another new initial structure which is not equilibrated and I got the same error. After changing pressure coupling from parrinello-rahman to berendsen , both the simulations went well. Nilesh Unstable models or unstable initial conditions will behave unpredictably. Unfortunately you've not given us much to go on. Mark On May 16, 2014 6:08 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Is there any prior equilibration? Using P-R for the initial phase of equilibration can be unstable. 4.0.7 was a bit more forgiving, and this same issue has been reported several times before with the 4.5.x series, with the solution being to set nstpcouple = 1 for the initial phase of equilibration with P-R. I did the simulations for two different initial structure. 1. Pre-equilibrated 2. New initial structure. Nilesh -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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. -- 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] Questions about position restraint for charged proteins
Hello. I am currently using GROMACS4.6.5 and trying to simulate a fluorescent protein(GFP,1EMB.pdb) fused to a muscarinic acetylcholine receptor(M2,3UON.pdb). PDB file of M2(3UON.pdb) included a lysozyme part(res#1002-1161), so I removed it to make the simulation consistent with our experimental data. As a result, there is a gap in M2 structure, which means M2 is divided into two chains(res#20-217, res#377-456), and when in NVT equilibration process, these chains move apart from each other because both are positively charged. I would like to keep the conformation of M2 and immobilize it in simulation to see only the motion of the fluorescent protein, so I applied position restrains to M2, but two chains still move away from each other and eventually I get many LINCS warnings during NVT equilibration process and simulation collapses. My question is: Position restrain is a proper way to keep conformations of proteins which have the same charge? Or is there any other way to do so? I am using all-bonds constraint and 2fs time step to save the simulation time. Other fundamental parameters are default. Any help would be appreciated. Thank you very much. Koki Below is the error messages during NVT equilibration process: --- relative constraint deviation after LINCS: rms 0.050664, max 3.739141 (between atoms 962 and 963) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 962963 89.90.1109 0.5118 0.1080 964965 90.10.1106 0.4336 0. 964966 31.90.1104 0.1199 0. Wrote pdb files with previous and current coordinates Step 575382, time 575.382 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 611.466194, max 51433.625000 (between atoms 570 and 573) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 555557 46.20.1345 0.1917 0.1345 557558 49.30.0997 0.1394 0.0997 557559 82.20.1430 0.4301 0.1430 559560 78.30.1080 0.3101 0.1080 559561 84.30.1538 1.6306 0.1538 559574 80.80.1490 0.3913 0.1490 561562 85.80. 1.4345 0. 561563 85.00. 1.3860 0. 561564 88.60.1538 7.0559 0.1538 564565 88.30. 6.1646 0. 564566 88.80.1538 6.5956 0.1538 564570 145.80.1538 18.8304 0.1538 566567 87.60. 1.7574 0. 566568 87.60. 1.7576 0. 566569 88.00. 1.7916 0. 570571 90.00. 10.2121 0. 570572 125.40. 10.2996 0. 570573 90.00. 5714.3872 0. 574575 42.60.1230 0.1646 0.1230 574576 42.10.1345 0.1834 0.1345 916917 33.80.0997 0.1182 0.0997 916918 115.00.1428 2.7045 0.1430 918919 92.60.1079 2.7119 0.1080 918920 149.60.1533 2.6632 0.1538 920921 36.50. 0.1355 0. 920922 35.70. 0.1401 0. 933934 106.00.1226 2.8814 0.1230 933960 86.30.1372 9.0101 0.1345 935962 121.30.1295 70.4373 0.1490 936940 172.60.1365 9.4523 0.1400 937955 150.40.1411 9.9921 0.1450 938939 43.20.1241 4.6305 0.1220 938940 79.60.1482 1.2946 0.1490 940941 48.90.1378 3.7713 0.1360 941942 42.80.1098 0.1650 0.1100 941943 33.20.1444 0.2096 0.1450 955956 73.30.1086 4.4738 0.1080 955957 68.80.1085 3.8836 0.1080 955958 43.40.1509 4.5246 0.1490 958959 33.60.1226 0.1674 0.1230 958969 36.30.1343 0.1844 0.1345 962963 103.50.5118 19.1058 0.1080 962964 131.90.1441 141.6376 0.1538 964965 88.90.4336 2773.4438 0. 964966 58.90.1199 82.5709 0. 964967 55.10.1502 133.7226 0.1420 967968 105.80.0947 47.8773 0.0960 Wrote pdb files with previous and current coordinates WARNING: Listed nonbonded interaction between particles 557 and 564 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for
Re: [gmx-users] berendsen vs parrinello-rahman
What Michael said, and if your .mdp setup triggers a code path for which the implementation changed between 4.0.7 and 4.5.5 (like it did for at least twin-range), then you should see different behaviour. But I guess we'll have to keep making unproductive guesses. Mark On Fri, May 16, 2014 at 11:25 PM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: One initial structure is equilibrated for 10ns using Gromacs VERSION 4.0.7. If I run same structure with same .mdp and same force field parameters using gromacs VERSION 4.5.5. I got the error system is blowing up. I made another new initial structure which is not equilibrated and I got the same error. After changing pressure coupling from parrinello-rahman to berendsen , both the simulations went well. Nilesh Unstable models or unstable initial conditions will behave unpredictably. Unfortunately you've not given us much to go on. Mark On May 16, 2014 6:08 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Is there any prior equilibration? Using P-R for the initial phase of equilibration can be unstable. 4.0.7 was a bit more forgiving, and this same issue has been reported several times before with the 4.5.x series, with the solution being to set nstpcouple = 1 for the initial phase of equilibration with P-R. I did the simulations for two different initial structure. 1. Pre-equilibrated 2. New initial structure. Nilesh -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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. -- 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
[gmx-users] mdrun error
Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line: 722 Fatal error: DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Please help me to understand this error.What this error is all about ? Where should I search to resolve this error ? Thanks Lovika -- 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.
