[gmx-users] About gmx msd and membrane leaflets
Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ¿How can separate the leaflets to know wich lipid are in each one? After ¿Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks -- 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] About membrane leaflets and msd
Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ¿How can separate the leaflets to know wich lipid are in each one? After ¿Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks -- 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] Error No Such Moleculetype System
Hello Gromacs users: im running the following command gmx grompp -p file.top -c solvated.gro -f minimization.mdp -o minimization.tpr but the following error appear: No such Molecule type system (line 16). I know this is about the topology, but i don see nothing strane in line 16. Line 16 is system. I hope can you help me. This is my topology: #include "martini_v2.2.itp" #include "Protein_A.itp" #include "Protein_B.itp" [ system ] ; name Martini system from 5iqp.pdb [ molecules ] ; namenumber Protein_A 1 Protein_B 1 System 1008 Protein 1008 Protein-H1008 C-alpha 0 Backbone 0 MainChain0 MainChain+cb 0 MainChain+H 0 SideChain1008 SideChain+H 1008 -- 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] About and index file of a monolayer...
Hello gromacs users: If i have a bilayer with lipids A & B and i want to create an index file for the upper and lower monolayer of one lipid, for example: lipid A-UPPER and lipid B-UPPER. Also, lipid A-LOWER and lipid B-UPPER. How can i do that using -n index.file? -- 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] About rdf in membranes
The -xy is after or before the .ndx. I have this command gmx rdf -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin Lemkul <jalem...@vt.edu> Enviado: martes, 20 de febrero de 2018 04:33 p. m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] About rdf in membranes On 2/20/18 7:03 PM, Poncho Arvayo Zatarain wrote: > > Hello Gromacs Users: I want to calculate rdf in membranes. I read i need > something like .xy and i´m a little confussed. The command will be: gmx rdf > -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg= What point is confusing? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html Justin Lemkul<http://www.biochem.vt.edu/people/faculty/JustinLemkul.html> www.biochem.vt.edu == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org To facilitate the communication between users and developers of GROMACS we have created different mailing lists that you can subscribe to. The lists are also archived ... * 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.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- 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] About rdf in membranes
Hello Gromacs Users: I want to calculate rdf in membranes. I read i need something like .xy and i´m a little confussed. The command will be: gmx rdf -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg= Thanks for your help -- 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] Problems with trjconv
Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n index -o file.gro -pbc whole but nothing happens. In index i use option System. What can i do to flip the bilayer? should i use lipid and water options in index? -- 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] Flip a bilayer
Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in vmd, is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n index -o file.gro -pbc whole but nothing happens. In index i use option System. What can i do to flip the bilayer? should i use lipid and water options in index? -- 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] Error in deuterium order parameters, index, nr
Hello gromacs users: i´m trying to graph my xvg of deuterium order parameters with the command: gmx order -s file.tpr -f fiile.xtc -n sn1.ndx -d z -od deuter_sn1.xvg but the following error appears: Error in user input: Invalid input lines in option nr. Required option was not provided and the default file "index" does not exist or is not accessible. The following extensions were tried to complete the file name: .ndx. Before that, to generate .ndx file i use the command: gmx make_ndx -f file.tpr -o sn1.ndx. What can i do to solve this? What is option nr? is necessary to use it? Thanks -- 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] Negative deuterium order parameters
Hello: I made 5 simulation: pure DPPC+a molecule inside, pure DPPE+molecule inside, 50% DPPC-50% DPPE+molecule inside, 75% DPPC-25%DPPE+molecule inside and 25%DPPC-75% DPPE+molecule inside. All the graphics were fine, but when i plot my system with 25%DPPC-755DPPE+Molecule inside the graphic of deuterium order parameters is not in order, is very disordered, with negative and positive values. Is it possible the molecule modifies the deuterium order parameters when i increase the DPPE %? Does anybody knows a reference i can read about this? Thanks. -- 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] Making a move using command gromacs/vmd
Hello gromacs user: i want to make a movie using a gromacs command. I use this: gmx trjconv -s file.gro -f file.trr -pbc -o no jump -ndec 7 -o movie.gro. But it mrks me the following error: command line -o does not exist. So, i erase -o on "-o no jump" and marks me the error: invalid command: no jump. What is the command to obtain movie.gro? Thank you. -- 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] Plotting area per lipid
Hello gromacs users: I have the area per lipids for my dppc-dppe-protein membrane. But i want to plot the area per lipid vs time of simulation. When i use GridMAT it appears by residue. Can i still use this program to plot rea per lipid vs time of simulation? How that works? I all still with aplvoro in command terminal and doesn´t work it. -- 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] Help: Illegal divion by zero lipid+protein+solvent
Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid types 1, resname 1 is DPPC, atomname 1 is P, resname2 and atomname 2 is none and solvent is TIP3. What could be the problem? Thanks -- 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] Illegal divion by zero lipid+protein+solvent
Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid types 1, resname 1 is DPPC, atomname 1 is P, resname2 and atomname 2 is none and solvent is TIP3. What could be the problem? Also, i run the same area per headgroup with dppc+solvent (with no protein) using the same atomname and resname and have no error. Or could i use the formula: APL = (box_x * box_y) / N_lipids_per_leaflet? Thanks -- 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] About msd and lateral diffussion command
Hello gromacs user: I want to obtain the msd and lateral diffussion for dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc -lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2 & 3 are dppc and dppe. Wht do you think about my command? It´s ok or is there anything wrong?. -- 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] Calculate area per head group
Hello Gromacs users: I know there is not about Gromacs, but i want to calculate area per headgroup through simulation time. Anybody knos about a tutorial of GridMAT or can help me please? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] area per headgroup over the course of simulation
Hello gromacs user: i want to obtain the area per headgroup over the course of simulation of a dppc, dppe and dppc/dppe membranes. Does anybody know how to obtain it with a gromacs 5.0.2 command or with GridMat? i think is using GridMat, but how? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Area per lipid through the time lipid membranes and mixed membranes
Hello gromacs user: I obtained the average area per lipid for dppc and dppe membrane, also for mixed membranes of dppc/dppe/embedded molecule. But i want to obtain the diagram of the area per lipid through the time, the course of my simulation for my dppc, dppe membranes and mixed membranes with a molecule inside. Is there any command in gromacs or what should i do? Thanks -- 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] Makeing movies using VMD
Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1. I finished my simulation and i have my tpr, xtc file, etc. How can i do the movie using vmd and algo save it and attach it for paste it in a powerpoint? I only can watch the trajectory in vmd, vut not save it and put it on a powerpoint. Do i need to use another program? Thanks -- 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] Error select a group gmx_density
Ok, thanks Justin. But i have one more question: What do you mean with syntax make_ndx? Is the way the command is writting: gmx_gpu density -ng 4 -f npt06.xtc -s npt06.tpr -o density.xvg? Is there anoher way to wrtie the command for density? De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin Lemkul <jalem...@vt.edu> Enviado: miércoles, 15 de febrero de 2017 08:02 a. m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Error select a group gmx_density On 2/15/17 10:55 AM, Poncho Arvayo Zatarain wrote: > > Hello Gromacs users: I´m trying to obtain the density og a mixed membrane > plus a protein. I use the command line: gmx_gpu density -ng 4 -f npt.xtc -s > npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION 5.0.4 > (single precision) > > Select 4 groups to calculate density for: Group 0 ( System) has > 58780 elements Group 1 ( Other) has 58780 elements Group 2 ( > PROTEIN) has 576 elements Group 3 ( DPPC) has 16640 elements > Group 4 ( DPPE) has 15488 elements Group 5 ( > TIP3) has 26076 elements Select a group: 3 & 4 & 2 & 5 Selected 3: 'DPPC' > Select a group: Error: No such group '&' Select a group: Selected 4: 'DPPE' > Select a group: Error: No such group '&' Select a group: Selected 2: > 'PROTEIN' Select a group: Error: No such group '&' Select a group: Selected > 5: 'TIP3' Last frame 5000 time 21.000 > > Read 5001 frames from trajectory. Calculating density > > Is there anything wrong with the command line or with Select a group: Error: > No such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the same > error but with | instead &? What about the Last frame 5000 time 21.000? You can't use make_ndx style syntax with gmx density. You should be prompted for 4 selections, individually. Otherwise, just calculate the density of each group separately. > Why 5000 and not 21.000?. Also, and .xvg file is generated Thanks > What should the time be? What is printed to the terminal is just a running indicator of progress; it is not a definitive statement of the contents of the trajectory. For that, use gmx check (or look in the .xvg file to see the time values). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul> Welcome to my site! - University of Maryland, Baltimore<http://mackerell.umaryland.edu/~jalemkul> mackerell.umaryland.edu Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above. == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them: * 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.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- 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] Error select a group gmx_density
Hello Gromacs users: I´m trying to obtain the density og a mixed membrane plus a protein. I use the command line: gmx_gpu density -ng 4 -f npt.xtc -s npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION 5.0.4 (single precision) Select 4 groups to calculate density for: Group 0 ( System) has 58780 elements Group 1 ( Other) has 58780 elements Group 2 (PROTEIN) has 576 elements Group 3 ( DPPC) has 16640 elements Group 4 ( DPPE) has 15488 elements Group 5 ( TIP3) has 26076 elements Select a group: 3 & 4 & 2 & 5 Selected 3: 'DPPC' Select a group: Error: No such group '&' Select a group: Selected 4: 'DPPE' Select a group: Error: No such group '&' Select a group: Selected 2: 'PROTEIN' Select a group: Error: No such group '&' Select a group: Selected 5: 'TIP3' Last frame 5000 time 21.000 Read 5001 frames from trajectory. Calculating density Is there anything wrong with the command line or with Select a group: Error: No such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the same error but with | instead &? What about the Last frame 5000 time 21.000? Why 5000 and not 21.000?. Also, and .xvg file is generated Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Trjconv problem invalid argument
Ok, so should i write trjconv before -ng 3, like gmx_gpu density trjconv -ng 3 -f file.xtc -s file.tpr -o out.xtc -skip 100 or donde write -ng in the command line? Thanks De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin Lemkul <jalem...@vt.edu> Enviado: martes, 14 de febrero de 2017 09:53 a. m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Trjconv problem invalid argument On 2/14/17 12:45 PM, Poncho Arvayo Zatarain wrote: > > > Hello Gromacs users: I want to obtain the density of a system using the > command: gmx_gpu density -ng trjconv -f file.xtc -s file.tpr -o out.xtc -skip > 100, but the following error appears: Invalid command argument: trjconv. What > is wrong with trjconv? I am using gromacs 5.0.3 > Nothing is wrong with trjconv, but your command is attempting to execute trjconv as an argument to gmx density -ng, which is complete nonsense. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul> Welcome to my site! - University of Maryland, Baltimore<http://mackerell.umaryland.edu/~jalemkul> mackerell.umaryland.edu Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above. == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them: * 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.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- 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] Trjconv problem invalid argument
Hello Gromacs users: I want to obtain the density of a system using the command: gmx_gpu density -ng trjconv -f file.xtc -s file.tpr -o out.xtc -skip 100, but the following error appears: Invalid command argument: trjconv. What is wrong with trjconv? I am using gromacs 5.0.3 Thanks -- 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] About gromacs density command
Hello gromacs user: i´m trying to obtain the membrane density of a dppc-dppe membrane, but i don´t know very well the command that i need to use. I have an idea: gmx_density -f file.xtc -n file.ndx -s file.tpr -ei file.dat -o file.xvg. File.dat corresponds to electrons.dat of dppc and/or dppe. Is this correct? -- 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] Gro file does not match topology file... continue
Hello: according to the queshere abouttion and the answer send me here about gro (58674) file does not mtch with the topology (58666), i checked my gro file at the top corner on the left and said 58674, and at the end of the file the number of molecules is the same, 58674. i used TIP3 model and 2 phospholipids: 26 dppe and 230 dppe also 8960 of TIP3. My top file is : Include forcefield parameters #include "toppar/charmm36.itp" #include "toppar/compound.itp" #include "toppar/DPPC.itp" #include "toppar/DPPE.itp" #include "toppar/TIP3.itp" [System] : Name Title [Molecules] : Compound #mols COMPOUND72 DPPE230 DPPC26 TIP3 8960 -- 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] Gro file does not match topology
Hello gromacs users: I´m trying to do a minimization with 26 dppc 230 dppe 8960 water and 72 molecules of a compound. But when i used grompp the following error appears: gro file (58674) does not match with top file (58666). Also i tried with 8961 molecules of solvent and the same error appears gro (58674) top (58669), 8962 solv gro (58674) top (58672), 8963 solv gro (58674) top (58675) and 8964 molecules of solvent and the same error appears with gro file (58674) and top file (58678). What can i do in this case? I read in the forum about divided the number by 3 but i don´t know how. My top is DPPC 26 DPPE 230 Compund 72 Water 8960 -- 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] Atomtype CG311 not found
Hello everyone: i´m trying to minimize a dppc-dppe-heta membrane, using charmm36. But when i use the grompp i have the following error: line: 1353 Fatal error: Atomtype CG311 not found. My topology includes: include "toppar/charmm36.itp" include "toppar/DPPE.itp" include "toppar/DPPC.itp" include "toppar/HETA.itp include "toppar/TIP3.itp [System] DPPC 26 DPPE 230 HETA 72 TIP3 72 Is there any relationship with my forcefield, the topology and the error that appears? -- 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] About negative values deuterium order parameters
Some days ago i send a quetion about negative values of deuterium order parameters in a 25% DPPC 75% DPPE+ nesthesic membrane. Thomas Piggot repond to me about the Scd que be negative too, specially for DPPC and DPPE. Now i send my obatained values for Scd. It is correct to have negative values? SN-1 and SN-3 correspond to DPPC and SN-2 and SN-4 correspond to DPPE. I watch the gro file in vmd and certainly look inclinable for the tails. All my other systems don´t have negative values like this one. Carbon DPPC64+DPPE192+AN-SN1 DPPC64+DPPE192+AN-SN2 DPPC64+DPPE192+AN-SN3 DPPC64+DPPE192+AN-SN4 1 -0.207868 0.156621-0.122543 0.202863 2 -0.199115 0.0507337 0.0757880.0911758 3 -0.129733 0.0328502 0.0638192 0.0722099 4 0.159087-0.0813808 0.0432806 0.0571403 5 -0.0940551 -0.0807225 -0.0842683 0.189616 6 -0.199373 -0.0259852 -0.0721477 0.167733 7 0.122858-0.0486781 0.00461267 0.132131 8 0.135019-0.0244167 -0.0931847 0.132473 9 0.1342240.0127981 0.0474575 0.143573 10 0.1350230.0502274 0.0901911 0.132179 11 0.128295-0.0841136 0.0882197 0.0943604 12 0.1252270.0756042 0.0349276 0.12459 13 0.1159380.220139-0.0766258 0.0861008 -- 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] Order parameters negative value
Hello: I´m analyzing the order parameters of a mixed membrane (25% dppc-75% dppe), but some of the values are negative and the graphic is not like the commons. Is this fine? the values for order parameters can be negative? what means negative values in an order parameters? -- 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] grp 1 does not have same number of elements as grp 1
Hello: I want to analyze order parameters for a 128 molecules of DPPC/ 128 moleculesDPPE/Drug membrane, but when i run gmx_order -s npt.tpr -f npt.xtc -n sn1.ndx -d z -od deuter_sn1.xvg, the following error appears: grp 1 does not have same number of elements as grp 1. I deleted 0-3 (System, DPPC, DPPE, Drug) and also 0-4 (System, DPPC, DPPE, Drug and TIP3)) and the error remains. What can i do in this case? Thanks -- 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] grp 1 does not have same number of elements as grp 1
Hello: I want to analyze order parameters for a 128 molecules of DPPC/ 128 moleculesDPPE/Drug membrane, but when i run gmx_order -s npt.tpr -f npt.xtc -n sn1.ndx -d z -od deuter_sn1.xvg, the following error appears: grp 1 does not have same number of elements as grp 1. I deleted 0-3 (System, DPPC, DPPE, Drug) and also 0-4 (System, DPPC, DPPE, Drug and TIP3)) and the error remains. What can i do in this case? Thanks -- 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] About atom references calculating area per lipid
hello: i´m trying to calculate area per lipid of mixed bilayer using Gid-MAT for a membrane of 128 DPPC and 128 DPPE and a mixed 128 DPPC+128 DPPE+Drug. My atom reference for DPPC is P, so ¿the atom reference for the DPPE need to be necesarili the P too?. Because when i run this, the result value of the area per lipid is the same for the mixed membrane and mixed+drug membrane. Also, i change the atom reference in DPPE for HS16660 and P for DPPC, this according the place occupies by P in DPPC, but the area per lipid is the same for mixed membrane and mixed membrane+drug. How i calculate or know my atom reference in case i have 2 phospholipids in a mixed bilayer? -- 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] About Area per lipid using Gid-MAT Continuation...
Hello Justin: Following with the error on my Grid-MAT-MD.pl line 761. This is my param_exampe using in Grid-MAT for calculate area per lipid in DPPC/DPPE bilayer Input file and input file parameters coord_file: dppc128+dppe128+hlt+tip3.gro file_type: gro num_frames:1 num_lipid_types: 2 resname1: DPPC atomname1: P8 resname2: DPPE atomname2: P8 Solvent: TIP3 Define the size and shape of the grid box_size: Vectors #override_vectors: 8.83600, 8.83600, 7.9 grid: 100 conserve_ratio: yes Define whether there is a protein embedded in the bilayer protein: yes precision: 1.3 value: 5.0 Defined the desire output files and format output_prefix: output output_format: vector thickness: yes area: yes top_pbc: yes bottom_pbc: yes average_pbc: yes top_areas: yes bottom_areas: yes -- 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] About Area per lipid using Gid-MAT
Hello: I'm calculating the area per lipid of a mixed bilayer of dppc and dppe
with a molecule inside, using GRID MAT. When i run Grid Mat it appears: Can't
calculate the are per lipid, line 761 can't divided by zero in GRID-MAT-MD.pl.
So, i check de Grid-MAT.pl in line 761 and this is in: Which is the line that
indicates can't divided by zero or which i have to modificate?
# Print APLs just based on number of lipids and cross-sectional surface area
print "\nCalculating area per lipid head group...\n";
my $area = $transfer_x*$transfer_y*100;
my $area_per_lipid_top = $area/(scalar(@top_leaflet_ref));
my $area_per_lipid_bottom = $area/(scalar(@bottom_leaflet_ref));
printf ("The lateral area of the system is %.5f sq. Angstroms (per
side)\n", $area);
print "When you don't account for any protein atoms:\n";
printf ("The average area per lipid in the top leaflet is %.5f sq.
Angstroms\n", $area_per_lipid_top);
printf ("The average area per lipid in the bottom leaflet is %.5f sq.
Angstroms\n", $area_per_lipid_bottom);
if ($param{protein} eq("yes")){
print "When you do take the protein atoms into account:\n";
--
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[gmx-users] About Area per lipids in Mixed Membranes
Hello: I want to calculate the area per lipids in DPPC/DPPE membranes of 128 lipids per leafleft. I have a membrane with 128 DPPC and 128 molecules ofDPPE and Box X and Box Y are 8.846591 and 8.846591 respectivelly. Should i calculate the area per lipid using (Box X * Box Y)/(#lipids per leafleft)? Also i have tha same membrane (128 molecules of DPPC and 128 molecules of DPPE) but with more than 50 molecules of a drug inside the membrane. Box X and Box Y are 9.118480 and 9.118480. Should i use Box X * Box Y)/(#lipids per leafleft) too? I´m using gromacs 5.0.2 -- 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] RV: About Deuterium order parameters
Hello gromacs users: I want to determine the deuterium order paramters for a dppc using gromacs 5.0.4 and i use the command: make_ndx -f npt.tpr -o sn1.ndx. Also i know that i need to do it too for sn2.ndx. But my question is: Should i make the index this way: > a C34 > a C36 > a C37 > a C38 ... > a C50 > del 0-21 > q But when i used this from C40-C50 it appears:the group is empty and wheen i use del 0-21 it appears that i remove system, other dppc, tip3, c34, c35, c36, c37, c38, c39, c40 and group 0-9 doesn´t exist But sn1.ndx appears. Is there anything wrong? or should i use: >a C34|>a C35...|>a C50|>del 0-21|q ? -- 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] About Deuterium order parameters
Hello gromacs user: I want to determine the deuterium order paramters for a dppc using gromacs 5.0.4 and i use the command: make_ndx -f npt.tpr -o sn1.ndx. Also i know that i need to do it too for sn2.ndx. But my question is: Should i make the index this way: > a C34 > a C36 > a C37 > a C38 ... > a C50 > del 0-21 > q But when i used this from C40-C50 it appears:the group is empty and wheen i use del 0-21 it appears that i remove system, other dppc, tip3, c34, c35, c36, c37, c38, c39, c40 and group 0-9 doesn´t exist But sn1.ndx appears. Is there anything wrong? or should i use: >a C34|>a C35...|>a C50|>del 0-21|q ? -- 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] Command line extend npt
Hello: This is my command lines when i want to extend to 50 ns: I´m using gpus gmx_gpu tpbconv -s npt.tpr -extend 5 npt02.tpr gmx_gpu mdrun -v -deffnm npt02 -cpi npt.cpt And the program (Gromacs 5.0.2) says: Can not open file: npt02.tpr Also, in my carpet i only have the npt.tpr, not npt02.tpr. Do i need change npt02 for npt.tpr? -- 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] About extend npt
Hello: this is my commands line De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Mark Abraham <mark.j.abra...@gmail.com> Enviado: miércoles, 14 de septiembre de 2016 10:44 a. m. Para: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Asunto: Re: [gmx-users] About extend npt Hi, We need to see your actual copied and pasted command lines and error messages before we can give feedback on what might be wrong. Mark On Wed, 14 Sep 2016 18:09 Poncho Arvayo Zatarain <poncho_8...@hotmail.com> wrote: > > > Hello. I did a 10 NPT but i want to extend to 50 ns and i´m using the > command gmx_gpu tpbconv file.tpr -extend 5 file02.tpr and mdrun -v > deffnm file02 -cpi npt.cpi. In my folder i only have the npt.tpr that i > think i should use as "tpr.file" but, what about file02.tpr and file02, > should i use npt.tpr too? Also, i use npt02.tpr as file02 and file02.tpr > but an error appears telling me that program can not run npt02.tpr but i > think is because i only have npt.tpr. I´m using gromacs 5.04. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. > 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] About extend npt
Hello. I did a 10 NPT but i want to extend to 50 ns and i´m using the command gmx_gpu tpbconv file.tpr -extend 5 file02.tpr and mdrun -v deffnm file02 -cpi npt.cpi. In my folder i only have the npt.tpr that i think i should use as "tpr.file" but, what about file02.tpr and file02, should i use npt.tpr too? Also, i use npt02.tpr as file02 and file02.tpr but an error appears telling me that program can not run npt02.tpr but i think is because i only have npt.tpr. I´m using gromacs 5.04. -- 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] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm
Hello: i'm running the grompp of NVT but during the run i have the following:NOTE: You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm, which is more than half the interaction ranges whereas switch functions are intended to act only close to the cut-offWhat does it means? it' ś anything wrong?My rlist, rcoulomb and rvdw are 1.2 (in nm), vdwtype: cut-off, vdwmodifier: force-switch, coulombtype: PME. Should i decrease rlist, rcoulomb and rvdw? increase my rlist to 1.4? or change my vdwtype to switch? Thanks -- 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] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps
Hello. I' ḿ simulating a DPPC membrane with TIP3 water model and charmm36 forcefield and in the grompp of NVT equilibration i have this warning: (Warning 1: file topol.top line 24) The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps. Maybe you forgot to change the constraints mdp option. What can i do to solve this? I attached mu nvt.mdp and topol.top. Also i have Note 1: rlist is equal to rvdw or/and rcoulomb. There is no explicit verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be neccesari for good energy conservation.Note 2: nstcommhttp://www.charmm-gui.org) v1.7 psf2itp.py Correspondance:;; j712l...@ku.edu or won...@ku.edu The main GROMACS topology file;; ; Include forcefield parameters#include "toppar/charmm36.itp"#include "toppar/DPPC.itp"#include "toppar/TIP3.itp" [ system ]; NameTitle [ molecules ]; Compound #molsDPPC256TIP38896 -- 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] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element
Hello, due to one of my last question and about the error: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. How can do large the box? My .gro files vectors are 8.9 8.90 and 7.90 and my cutoff lenghts are: nstlist = 10 ; 10 fsrlist= 1.2 ; short-range neighborlist cutoff (in nm)rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)rvdw = 1.2 ; short-range van der Waals cutoff (in nm)vdwtype = cutoff -- 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] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element
Hello, i ḿ working in a lipid bilayer using charmm36 forcefield and trying to do NVT equilibration but when i use grompp for nvt i receive the folowing error: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I read about this at Manual of Gromacs and decrease the rlist but the error is still there. The other solution is to increase the box size but, it is safe to do this? or what can i do? i can attach my nvt.mdp file if you wantThanks -- 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] Segmentation fault (core dumped) after grompp minimization
Hello, i'm working with a 256 phospholipid membrane and i run grompp for minimization and to generate a .tpr file, so after run grompp i run the mdrun but instantly crushed with the legend: SSteepest Descents: Tolerance Fmax: 1.e03. No. of steps: 50,000, nan Fmax: inf, atom: 30983. Segmentation fault (core dumped). It could be by the cluster i ' m using? These are the characteristics: 512 cores CPU, 8 GPU'S, 2 visualization notes. Or it is like a Gromacs bug? Iḿ running in Gromacs 5.0.4. Or i have an error at atom 30983? I attached my .mdp file that i used for grompp of miniization. How can i solve it?Thanks -- 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] Tau-t should be at least 20 times larger than nsttcouple*dt
Hello users: I want to run a simulation with MD run of DPPC+DPPE+Ligand+Water using the command gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr but when i used it the following warning and error appears:Warning: For proper integration of the Nose-Hoover thermostat, tau-t (0.1) should be at least 20 times larger than nsttcouple*dt (0.01)Fatal error: Too many warnings(1), gmx terminated.Could you help me please?My mdp file is the following:title = DPPC+DPPE+LIGAND Production MD ; Run parametersintegrator = md; leap-frog integratornsteps = 50; 2 * 50 = 1000 ps (1 ns)dt = 0.002 ; 2 fs; Output controlnstxout = 1000 ; save coordinates every 2 psnstvout= 1000 ; save velocities every 2 psnstxtcout = 1000 ; xtc compressed trajectory output every 2 psnstenergy = 1000 ; save energies every 2 psnstlog= 1000 ; update log file every 2 ps; Bond parameterscontinuation = yes ; Restarting after NPT constraint_algorithm = linc s ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighborsearchingns_type= grid ; search neighboring grid celsnstlist = 5 ; 10 fsrlist = 1.2 ; short-range neighborlist cutoff (in nm)rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)rvdw = 1.2 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order= 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature coupling is ontcoupl= Nose-Hoover ; More accurate thermostattc-grps= DPPC DPPE LIG TIP3 ; fourth coupling groups - more accuratetau_t= 0.5 0.5 0.5 0.1 ; time constant, in psref_t = 303 303 303 303 ; reference temperature, one for each group, in K; Pressure coupling is onpcoupl = Parrinello-Rahman ; Pr essure coupling on in NPTpcoupltype= semiisotropic ; uniform scaling of x-y box vectors, independent ztau_p= 2.0 ; time constant, in psref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr= EnerPres ; account for cut-off vdW scheme; Velocity generationgen_vel = no; Velocity generation is off; COM motion removal; These options remove motion of the protein/bilayer relative to the solvent/ionsnstcomm = 1comm-mode = Linearcomm-grps = DPPC DPPE LIG TIP3 -- 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] Nvt T-coupling error
I`m running a simulation of dppe+dppe+ligand+wáter and i`m building index with the command gmc make_ndx –f minimiz-gro –o index.ndx. When i use the command the following options appears to build the index: 0 System27592 atoms 1 Other 27592 atoms 2 LIG 8 atoms 3 DPPC 8320 atoms 4 DPPE 7744 atoms 5 TIP3 11520 atoms And i selected 3| 4 | 2 | 5 and creates the group DPPC_DPPE_LIG_TIP3 with 27592 atoms. Then i used the command instruction gmx grompp -f nvt.mdp -c minimiz.gro -p dppc+dppe+ligand+water.top -n index.ndx -o nvt.tpr, i run it and the following error appears: Fatal error: 11520 atoms are not part of any of the T-coupling groups. Could anybody help me to solve the error please? My nvt.mdp is the following: title = NVT equilibration for DPPC-DPPE-LIGANDdefine = -DPOSRES ; position restrain the protein; Run parametersintegrator = md; leap-frog integratornsteps= 5 ; 2 * 5 = 100 psdt = 0.002 ; 2 fs; Output controlnstxout = 100 ; save coordinates every 0.2 psnstvout = 100 ; save velocities every 0.2 psnstenergy = 100 ; save energies every 0.2 psnstlog = 100 ; update log file every 0.2 ps; Bond parameterscontinuation = no; first dynamics runconstraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighborsearchingns_type= grid ; search neighboring grid celsnstlist = 5 ; 10 fsrlist= 1.2 ; short-range neighborlist cutoff (in nm)rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)rvdw = 1.2 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order= 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature coupling is ontcoupl= V-rescale ; modified Berendsen thermostattc-grps = DPPC DPPELIG ; three coupling groups - more accuratetau_t= 0.1 0.1 0.1 ; time constant, in psref_t = 303 303 303 ; reference temperature, one for each group, in K; Pressure coupling is offpcoupl = no; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr= EnerPres ; account for cut-off vdW scheme; Velocity generationgen_vel= yes ; assign velocities from Maxwell distributiongen_temp = 323 ; temperature for Maxwell distributiongen_seed = -1; generate a random seed; COM motion removal; These options remove motion of the protein/bilayer relative to the solvent/ionsnstcomm= 1comm-mode= Linearcomm-grps = DPPC_DPPE LIG -- 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] DPPC hlothane Residue DPP not found in residue topology database
Hello: Concerning about my last question of DPPC membrane and halothane simulation and the GROMOS 53a6. When i used pdb2gmx the following error appears: Residue DPP not found in residue topology database. Then, i googled to Gromacs webpage and i found XXX'_not_found_in_residue_topology_database. So, after that and because a suggestion that probably GROMOS53a6 is not the best stock for simulate membranes, i tried every option of forcefield that GROMACS presented to me: Amber93 protein Amber94 nucleic, Amber94 forcefield, Amber96 protein nucleic Amber94, Amber99 protein nucleic Amber94, Amber99SB Protein, nucleic Amber 94, AmberGS forcefield, CHARMM27 all-atom forcefield, Gromos96 43a1, 43a2, 45a3, 53a5, 53a6, 54a7 and OPLS-AA/L and the same error appears in every orcefield: Residue DPP not found in residue topology database. What can i do? Because i simulated an Apoferritin-halothane and DPPC membrane with water and used GROMOS5a6 and everything was fine, but not this time. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Protein-ligand error pdb2gmx
Hello: I made the Apoferritin-T4 Lysozyme tutorial of Justin, then i change the ligand and simulated Apoferritin with an anaesthesic (halothane) and everything is fine. I tried to run a third simulation using halothane as ligand and DPPC instead of Apoferritin. I have a folder of gromos53a6.ff with all the parameters of this forcefield. But when i try to run pdb2gmx, the following error appears: Fatal error: "Residue DPP not found in residue topology database". The only different thing i did was aggregate the gromos53a6.ff folder and change Apoferritin for DPPC (i obtained DPPC.pdb and dppc.itp structure from P. Tieleman webpage). How can i solve this error? -- 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] Fatal error pdb
Hello: I'm trying to simulate an halothane molecule in water. I download the halothane at pubchem and converted to pdb format using open babel 2.3.2 but when i use pdb2gmx and select OPLS/AA forcefield it appears: Fatal error: halothane.pdb. Could you help me please? is there any problem with my pdb?. This is my pdb format: COMPND3562 AUTHORGENERATED BY OPEN BABEL 2.3.2 HETATM1 BR LIG 1 1.825 -1.412 -0.043 1.00 0.00 Br HETATM2 CL LIG 1 1.493 1.601 -0.049 1.00 0.00 Cl HETATM3 F LIG 1 -1.442 0.983 0.438 1.00 0.00 F HETATM4 F LIG 1 -0.715 -0.052 -1.340 1.00 0.00 F HETATM5 F LIG 1 -1.239 -1.182 0.454 1.00 0.00 F HETATM6 C LIG 1 -0.666 -0.040 0.010 1.00 0.00 C HETATM7 C LIG 1 0.744 0.102 0.530 1.00 0.00 C HETATM8 H LIG 1 0.765 0.103 1.623 1.00 0.00 H CONECT17 CONECT27 CONECT36 CONECT46 CONECT56 CONECT63457 CONECT6 CONECT71268 CONECT7 CONECT87 MASTER0000000 08080 END -- 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] No such moleculetype DPPE
Hello: i'm working in a simulation for a DPPC/DPPE membrane and when i use the instruction grompp -f minim.mdp -c dppc-dppe128.pdb -p topol_dppc.top -o em.tp for enrgy minimization, the following error appears: Fatal error: No such moleculetype DPPE, so it appears some warnings like: File ffnonbonded.itp, line 67: Overriding atomtype NUrea. Could you help me please? -- 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] DPPC/DPPE minim.mdp
Hello, i want to simulate a 128 DPPC molecule, 3655 water molecules but with 25% of DPPE. I replace de 25% of 128 DPPC molecules with DPPE and i'ḿ using the same forcefield and topology reported by Lemkul in his KALP15 in DPPC tutorial. When i want to minimize the energy i use the command line: gmx grompp -f minim.mdp -c dppc-dppe128.pdb -p topol_dppc.top -o em.tp but the following error appears: Input/output error: minim.mdp. How can i solve it? Is correct to use the same forcefield and topology? I'm using Gromacs 5.0.4. This in my minim.mdp file ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) -- 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] gmx distance
Helecho 3 4| g_distlo, i want to introduce a coomand in Gromacs 5.0.4 with the initial echo 3 4| g_dist. Should i use gmx distance echo 3 4| g_dist and the rest of the commnand? This is the complete command i want to use echo 3 4| g_dist -f dppc128_1-nj-ct-nobox.xtc -s dppc128_1.tpr -o dppc128-Dpp.xvg -n Dpp.ndx -b 2. Or how should i use that command on gromacs 5.0.4? Because i read the g_dist in gromacs 5.0 has been modified. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_dist tools
Hello, i want to run this command: echo 3 4| g_dist -f dppc128_1-nj-ct-nobox.xtc - s dppc128_1.tpr -o dppc128-Dpp.xvg -n Dpp.ndx -b 2 in Gromacs 5.0.4 but when i run it, the following appears: This tool has been removed. Please see tool changes for 5.0. And when i see th tools appears: g_dist: This tool has been removed in 5.0. A replacement is gmx distance (for most options) or gmx select (for -dist or -lt).If you had index groups A and B in index.ndx for g_dist, you can use the following command to compute the same distance with gmx distance:gmx distance -n index.ndx -select 'com of group A plus com of group B' -oxyz -oall The -intra switch is replaced with -nopbc. If you used -dist D, you can do the same calculation with gmx select: gmx select -n index.ndx -select 'group B and within D of com of group A' -on/-oi/-os/-olt You can select the output option that best suits your post-processing needs (-olt is a replacement for g_dist -dist -lt) Shoukd i use -dist or -intra option? -- 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] Invalid command line argument
Hello: I'm doing Martínez Seara simulation and i want to run this command: echo 0|trjconv -f dppc128_1-nj-ct.xtc -s dppc128_1.tpr -o dppc128_1-nj -ct -nobox.xtc -box 100 100 100 but it appears: Invalid command line argument: -nobox.xtc Iḿ using GROMACS 5.0.2 and working in a cluster. What can i do? Alfonso -- 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] gromos53a6_lipid.ff/forcefield.itp not found
From: poncho_8...@hotmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: gromos53a6_lipid.ff/forcefield.itp not found Date: Wed, 27 May 2015 14:50:27 -0300 Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr i have this: Fatal error: Topology include file gromos53a6_lipid.ff/forcefield.itp not found. What should i include in my topolofy files? And i have 2 notes: NOTE 1 [file dppc128.mdp, line 34]: dppc128.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Should i inlude Cutoff-scheme verlet in my mdp file? NOTE 2 [file dppc128.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Should i include Berendsen at my Tcouple option on mdp file? -- 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] gromos53a6_lipid.ff/forcefield.itp not found
Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr i have this: Fatal error: Topology include file gromos53a6_lipid.ff/forcefield.itp not found. What should i include in my topolofy files? And i have 2 notes: NOTE 1 [file dppc128.mdp, line 34]: dppc128.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Should i inlude Cutoff-scheme verlet in my mdp file? NOTE 2 [file dppc128.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Should i include Berendsen at my Tcouple option on mdp file? -- 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] trjconv command not found
Hello, when i use the command echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 i have this: command not found: trjconv. What can i do? Alfonso -- 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] .gro error
Hello, i'm working on membrane thickness in Martínez-Seara dppc article. When i use the following command: printf %s\n r 1-64 a P r 65-128 a P q|make_ndx -f dppc128_1.gro -o Dpp.ndx The following error appears: File Input/output error: dppc128_1.gro. Could you help me to solve it please? Alfonso -- 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] Version 100 with version 83 program
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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] Version 100 with version 83 program
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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] Re generate a tpr file
i'm trying to use the following command echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 but it appears the following error reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I'm doing Martinez Seara tutorial and in the article uses 4.0.2 gromacs and i'm using gromacs version 4.6.5. How can i re generate the article in my 4.6.5 version? Alfonso -- 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] Version 100 with version 83 program
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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] Fatal error tpx file
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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] Syntax error -File dppc.itp line 1
Hello, im doing a DPPC simulation and when i use grompp to generate tpr file this appears: Fatal error: Syntax error -File dppc.itp, line 1. Last line read: '[moleculetype]' Invalid order for directive moleculetype. What can i do? My dppc.itp includes [ moleculetype ] ; Name nrexcl DPPC 3 [ atoms ], [ pairs ], [ dihedrals ] #ifdef POSRES_LIPID #include lipid_posre.itp #endif And my topology file is: ; Include chain topologies #include dppc.itp #include ffG53a6.itp #include dppc_53a6.itp ; Include water topology #include spc.itp ; Include ion topologies #include gromos53a6_lipid.ff/ions.itp ; System specifications [ system ] DPPC Bilayer, [ molecules ] ; molecule name nr. DPPC 128 SOL 3655 -- 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] File input/output error: algorithm_parameters.mdp
Hello, i´m working in a tutorial to generate a tpr file and i´m using grompp, my mdp file, .pdb and .top file, -o and .tpr file. I´m using this command for grompp: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr And it appears two errors: File input/output error: algorithm_parameters.mdp Fatal error: Topology include file dppc.itp not foundAnd actually i have the dppc.itp inside a file called gromos53a6_lipid.ff with more itp files -- 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] FW: Sending an email, question
Hello, i I´m trying to replicate a DPPC128 membrane simulation of the Article Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It of Martínez-Seara et al. This is mi mpd file and i´m using GROMACS 5.0.2 Title: MD SIMULATIONintegrator : md dt : 0.002 nsteps : 1 nstxout : 5 nstvout : 5 nstlog : 5000 nstenergy : 5000 nstxtcout : 5000 pbc : xyz coulombtype : PME rcoulomb : 1.0 rvdw : 1.4 tcoupl : Berendsen tc-grps : System tau_t : 0.1 ref_t : 325 Pcoupl : Berendsen Pcoupltype : semiisotropic tau_p : 2.0 2.0 ompressibility : 4.5e-5 4.5e-5 ref_p : 1.0 1.0 constraints : all-bonds When i use grompp of the article: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr (acoording to the names of my files) i got this error: Command line: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr NOTE 1 [file dppc128.mdp, line 49]: dppc128.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Ignoring obsolete mdp entry 'title'Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' ERROR 1 [file dppc128.mdp]: With Verlet lists rcoulomb!=rvdw is not supported NOTE 2 [file dppc128.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Setting the LD random seed to 772888378 ---Program grompp, VERSION 5.0.2Source code file: /root/GROMACS/gromacs-5.0.2/src/gromacs/gmxpreprocess/gmxcpp.c, line: 311 Fatal error:Topology include file dppc.itp not foundFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--- -- 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] Sending an email, question
Hello, i´m new here and i have a question. I´m trying to replicate a DPPC128 membrane simulation of the Article Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It of Martínez-Seara et al. This is mi mpd file and i´m using GROMACS 5.0.2 Title: MD SIMULATIONintegrator : md dt : 0.002 (b) nsteps : 1 nstxout : 5 nstvout : 5 nstlog : 5000 nstenergy : 5000 nstxtcout : 5000 pbc : xyz coulombtype : PME rcoulomb : 1.0 rvdw : 1.4 tcoupl : Berendsen tc-grps : System tau_t : 0.1 ref_t : 325 Pcoupl : Berendsen Pcoupltype : semiisotropic tau_p : 2.0 2.0 compressibility : 4.5e-5 4.5e-5 ref_p : 1.0 1.0 constraints : all-bonds When i use grompp of the article: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr (acoording to the names of my files) i got this error: Command line: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr NOTE 1 [file dppc128.mdp, line 49]: dppc128.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Ignoring obsolete mdp entry 'title'Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' ERROR 1 [file dppc128.mdp]: With Verlet lists rcoulomb!=rvdw is not supported NOTE 2 [file dppc128.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Setting the LD random seed to 772888378 ---Program grompp, VERSION 5.0.2Source code file: /root/GROMACS/gromacs-5.0.2/src/gromacs/gmxpreprocess/gmxcpp.c, line: 311 Fatal error:Topology include file dppc.itp not foundFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--- -- 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.
