[gmx-users] genconf command
Dear Gmx-users, I created a box size 4 4 2 and named layer.gro. Then "genconf" was used to doulble this box: genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8 However, the copied box has the same direction as the original box. Could you please help me to rotate 180 degrees the copied one? Thank you very much. Best regards, Cuong -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation Box type
On 17/07/2012 4:16 PM, tarak karmakar wrote: Dear All, I want to opt for the rhombic dodecahedron box in my simulation of a protein. I am using the following command to select the type of the box "editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron" but after this if I'm seeing this protein system within the box in VMD but its not showing that dodecahedron box, instead showing rectangular one. I don't know whether I am giving the wrong command or it's coming out from VMD software. So can anyone give suggestion regarding this problem so that I can make myself confirmed by seeing the exact box, I need to have, prior to the simulation. This is normal (discussed often in the archives). The box is specified by its vectors, not by the atomic coordinates, and the triclinic box you can see with VMD is equivalent to what you chose (e.g. a 2D tiling with hexagons can be represented as a 2D tiling of rhombuses). You can see trjconv -h about -ur to change the coordinates for visualization purposes. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Simulation Box type
Dear All, I want to opt for the rhombic dodecahedron box in my simulation of a protein. I am using the following command to select the type of the box "editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron" but after this if I'm seeing this protein system within the box in VMD but its not showing that dodecahedron box, instead showing rectangular one. I don't know whether I am giving the wrong command or it's coming out from VMD software. So can anyone give suggestion regarding this problem so that I can make myself confirmed by seeing the exact box, I need to have, prior to the simulation. Thanks in advance, Tarak -- Tarak Karmakar Molecular Simulation Lab. C.P.M.U JNCASR -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with Inflategro!!!
On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the "building unit cell" part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do "Inflategro" to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem with Inflategro!!!
Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the "building unit cell" part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do "Inflategro" to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! ~Saravanan -- MSS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Possible problem with g_hbond
On 7/16/12 10:59 AM, Andrew DeYoung wrote: Hi, If you have time, I'm wondering if you can please help me to think through a problem that I seem to be having with g_hbond. I am looking for a way to list the _individual_ hydrogen bonds as a function of time, by indices -- more than just determining the number of hydrogen bonds at every timestep. So, at every timestep, I would like to somehow list the hydrogen bonds that exist during that time. At timestep 1, for example, a hydrogen bond might exist between oxygen26 and hydrogen353. But at timestep 2, this same hydrogen bond may no longer exist because oxygen26 and hydrogen353 have drifted beyond the cutoff. At timestep 3, the hydrogen bond may exist again because the atoms have drifted together. Do you know if generating such a list is possible, perhaps with g_hbond? I was thinking that perhaps such information would be listed in the log file, which, according to the manual, is output using the -g flag. So, I have tried the following command in g_hbond_d (I had run double precision simulations): g_hbond_d -f traj.trr -s topol.tpr -n index.ndx -g test.log (I select two non-overlapping groups in index.ndx when prompted.) I also tried the same without "_d": g_hbond -f traj.trr -s topol.tpr -n index.ndx -g test.log But in both cases, I do not obtain test.log or any log file; I only obtain hbnum.xvg from the -num flag, which is non-optional output. Have you ever experienced the -g flag apparently not working in g_hbond? Do you have any thoughts about what I can try differently? Thanks! The output you want is contained in the .xpm file produced with the -hbm flag, and the hydrogen bonds are listed in the index file produced by -hbn. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Possible problem with g_hbond
Hi, If you have time, I'm wondering if you can please help me to think through a problem that I seem to be having with g_hbond. I am looking for a way to list the _individual_ hydrogen bonds as a function of time, by indices -- more than just determining the number of hydrogen bonds at every timestep. So, at every timestep, I would like to somehow list the hydrogen bonds that exist during that time. At timestep 1, for example, a hydrogen bond might exist between oxygen26 and hydrogen353. But at timestep 2, this same hydrogen bond may no longer exist because oxygen26 and hydrogen353 have drifted beyond the cutoff. At timestep 3, the hydrogen bond may exist again because the atoms have drifted together. Do you know if generating such a list is possible, perhaps with g_hbond? I was thinking that perhaps such information would be listed in the log file, which, according to the manual, is output using the -g flag. So, I have tried the following command in g_hbond_d (I had run double precision simulations): g_hbond_d -f traj.trr -s topol.tpr -n index.ndx -g test.log (I select two non-overlapping groups in index.ndx when prompted.) I also tried the same without "_d": g_hbond -f traj.trr -s topol.tpr -n index.ndx -g test.log But in both cases, I do not obtain test.log or any log file; I only obtain hbnum.xvg from the -num flag, which is non-optional output. Have you ever experienced the -g flag apparently not working in g_hbond? Do you have any thoughts about what I can try differently? Thanks! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Σχετ: [gmx-users] umbrella sampling
On 7/16/12 10:39 AM, Giovani Mancini wrote: Dear Justin, Thank you very much for your immediate response to my e-mail. I am trying to conduct umbrella sampling simulations of a molecule into a lipid bilayer (DLPC) along the z-axis. As a reference, I used your tutorial which is well-written and provide useful information of how to set up the system in GROMACS. I'm glad you found it useful. You almost certainly want cylindrical restraints, which are described in the manual, section 6.3 with corresponding Figure 6.2 to illustrate its principles. The overall workflow is very similar to the tutorial, but the contents of the .mdp files will be quite different. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Σχετ: [gmx-users] umbrella sampling
Dear Justin, Thank you very much for your immediate response to my e-mail. I am trying to conduct umbrella sampling simulations of a molecule into a lipid bilayer (DLPC) along the z-axis. As a reference, I used your tutorial which is well-written and provide useful information of how to set up the system in GROMACS. Best regards Grigoris - Αρχικό μήνυμα - Απο: Justin Lemkul Προς: Giovani Mancini ; Discussion list for GROMACS users Κοιν.: Στάλθηκε: 5:29 μ.μ. Δευτέρα, 16 Ιουλίου 2012 Θεμα: Re: [gmx-users] umbrella sampling On 7/16/12 10:25 AM, Giovani Mancini wrote: > Dear Gromacs users, > > I just read the tutorial by Justin Lemkul about umbrella sampling simulations > along z-axis. My question is whether we need cylindrical confinement of the > molecule that is pulling away from a reference molecule. > Thanks in advance > The tutorial is a very simple system designed to get users familiar with a basic workflow. There are more elegant ways of doing umbrella sampling for more complicated systems. Cylindrical restraints can be useful in some cases and are discussed in the manual. Without knowing more about the system you're considering, it's hard to provide specific advice. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella sampling
On 7/16/12 10:25 AM, Giovani Mancini wrote: Dear Gromacs users, I just read the tutorial by Justin Lemkul about umbrella sampling simulations along z-axis. My question is whether we need cylindrical confinement of the molecule that is pulling away from a reference molecule. Thanks in advance The tutorial is a very simple system designed to get users familiar with a basic workflow. There are more elegant ways of doing umbrella sampling for more complicated systems. Cylindrical restraints can be useful in some cases and are discussed in the manual. Without knowing more about the system you're considering, it's hard to provide specific advice. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] umbrella sampling
Dear Gromacs users, I just read the tutorial by Justin Lemkul about umbrella sampling simulations along z-axis. My question is whether we need cylindrical confinement of the molecule that is pulling away from a reference molecule. Thanks in advance Best regards, Giovani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Some interactions seem to be assigned multiple times
On 13/07/2012 7:05 PM, Shima Arasteh wrote: Dear gmx users, My system is composed of a protein and water. I am working with CHARMM36 and the current version of Gromacs, 4.5.5. For NVT equilibration , I get this error: "Software inconsistency error: Some interactions seem to be assigned multiple times" Through the mailing list, I just found that some bugs might be the reason of the error, and the Gromacs version should be current. But as I said I use the current version of Gromacs. I really don't have any idea for solving this problem. This is rare, but IIRC usually a symptom of blowing up. Try searching the mailing list. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT with shape fluctuations
On 13/07/2012 9:56 PM, J Benet wrote: Hi, I would like to know if it's possible to perform an NVT simulation but letting the box shape to fluctuate. Probably possible, but not implemented. What physical conditions would it model? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positions and velocities from trajectory for restart
On 7/16/12 7:19 AM, Inon Sharony wrote: Good afternoon. g_traj has the option to output position coordinates (-ox) OR velocity coordinates (-ox) from an input trajectory file. The former can even be output to a trajectory file format, trr/trj/cpt (-oxt). I would like to restart a simulation using a separate set of MD parameters (mdp) from the phase-space point in a given time frame of a previous trajectory. I need BOTH position and velocity coordinates to fully reproduce the system in phase-space. Non of the above cited options suffice, since they give me only one of the two (positions OR velocities) but not both. Ideally, I would like to use something like g_traj -f traj-old -s topol -b $t_init -e $t_final -ot traj-new -fp To create a new trajectory file "traj-new.trr" which contains both positions and velocities which appear in "traj-old.trr" between time-frames $t_init and $t_final (this could be only one time-frame), where the currently non-existent g_traj option "-ot" outputs both positions and velocities from one trajectory to another. Is there a way to do this now? If not, could you possibly implement such an option? The -ot option is not non-existent, it's just unrelated to what you want to do, and it does not write a trajectory. "Option -ot plots the temperature of each group, provided velocities are present in the trajectory file. No corrections are made for constrained degrees of freedom! This implies -com." From the GMX website I understand that re-starting simulations is being pushed towards using checkpoint (cpt) files rather than trr. However, when I tried to see if the velocities get copied to the cpt file, I got: $ echo 0 | g_traj_d -f traj.trr -s topol.tpr -oxt traj.cpt -fp \001\001 "Source code file: trxio.c, line: 269 \001\001 Fatal error: Sorry, write_trxframe_indexed can not write cpt" Does the -oxt option work to produce a .trr file? If you just want individual states from which to continue the simulation, you don't need g_traj at all. Just use trjconv -dump to drop out individual frames from the .trr file, which will contain coordinates and velocities present in the .trr file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: נושא: RE: Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain
I thought setting tau_t=0 for some of the groups means that they're not coupled. That is tau_t would in fact be infinite, but that would be more difficult to input, whereas if tau_t were actually equal to zero the situation (as you described it) would lack physical significance... Since only the Nose-Hoover thermostat gave me any trouble with setting tau_t=0, I thought this was already set as described above for all other thermostats (not including the SD thermal-coupling scheme). This was addressed in the past by Mark, David, you and myself : http://gromacs.5086.n6.nabble.com/SD-temperature-coupling-groups-tp4388610p4388614.html And also: http://gromacs.5086.n6.nabble.com/Temperature-de-coupling-in-Langevin-Dynamics-tp4457944.html If my system is [ 0 1 ], my t coupl grps are [ 0 1 ] (i.e. diatomic, thermal-coupling group for each atom), and I want to tell GMX to thermally couple atom 1 with tau_t=1ps and NOT couple atom 0 at all: How would I do so in v-rescale? How would I do so in Nose-Hoover? How would I do so in SD? -- View this message in context: http://gromacs.5086.n6.nabble.com/RE-Discontinuity-in-first-time-step-velocities-for-diatomic-molecule-locally-coupled-to-thermal-drain-tp4999293p4999449.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positions and velocities from trajectory for restart
Correction -- in the first sentence: "... velocity coordinates (-ov) ..." Inon Sharony J+N+W+N% ShR+W+N+J+ [1]http://atto.TAU.ac.IL/~InonShar +972-3-640-7634 On 07/16/2012 02:19 PM, Inon Sharony wrote: Good afternoon. g_traj has the option to output position coordinates (-ox) OR velocity coordinates (-ox) from an input trajectory file. The former can even be output to a trajectory file format, trr/trj/cpt (-oxt). I would like to restart a simulation using a separate set of MD parameters (mdp) from the phase-space point in a given time frame of a previous trajectory. I need BOTH position and velocity coordinates to fully reproduce the system in phase-space. Non of the above cited options suffice, since they give me only one of the two (positions OR velocities) but not both. Ideally, I would like to use something like g_traj -f traj-old -s topol -b $t_init -e $t_final -ot traj-new -fp To create a new trajectory file "traj-new.trr" which contains both positions and velocities which appear in "traj-old.trr" between time-frames $t_init and $t_final (this could be only one time-frame), where the currently non-existent g_traj option "-ot" outputs both positions and velocities from one trajectory to another. Is there a way to do this now? If not, could you possibly implement such an option? From the GMX website I understand that re-starting simulations is being pushed towards using checkpoint (cpt) files rather than trr. However, when I tried to see if the velocities get copied to the cpt file, I got: $ echo 0 | g_traj_d -f traj.trr -s topol.tpr -oxt traj.cpt -fp \001\001 "Source code file: trxio.c, line: 269 \001\001 Fatal error: Sorry, write_trxframe_indexed can not write cpt" -- Inon Sharony J+N+W+N% ShR+W+N+J+ [2]http://atto.TAU.ac.IL/~InonShar +972-3-640-7634 References Visible links 1. http://atto.tau.ac.il/~InonShar 2. http://atto.tau.ac.il/%7EInonShar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Positions and velocities from trajectory for restart
Good afternoon. g_traj has the option to output position coordinates (-ox) OR velocity coordinates (-ox) from an input trajectory file. The former can even be output to a trajectory file format, trr/trj/cpt (-oxt). I would like to restart a simulation using a separate set of MD parameters (mdp) from the phase-space point in a given time frame of a previous trajectory. I need BOTH position and velocity coordinates to fully reproduce the system in phase-space. Non of the above cited options suffice, since they give me only one of the two (positions OR velocities) but not both. Ideally, I would like to use something like g_traj -f traj-old -s topol -b $t_init -e $t_final -ot traj-new -fp To create a new trajectory file "traj-new.trr" which contains both positions and velocities which appear in "traj-old.trr" between time-frames $t_init and $t_final (this could be only one time-frame), where the currently non-existent g_traj option "-ot" outputs both positions and velocities from one trajectory to another. Is there a way to do this now? If not, could you possibly implement such an option? From the GMX website I understand that re-starting simulations is being pushed towards using checkpoint (cpt) files rather than trr. However, when I tried to see if the velocities get copied to the cpt file, I got: $ echo 0 | g_traj_d -f traj.trr -s topol.tpr -oxt traj.cpt -fp \001\001 "Source code file: trxio.c, line: 269 \001\001 Fatal error: Sorry, write_trxframe_indexed can not write cpt" -- Inon Sharony J+N+W+N% ShR+W+N+J+ [1]http://atto.TAU.ac.IL/~InonShar +972-3-640-7634 References Visible links 1. http://atto.tau.ac.il/~InonShar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints in SMD
On 7/16/12 5:36 AM, Raj wrote: Hi all, It may be naive but I would like to get some clear explanation in SMD ( COM pulling) reg. The question is, Before performing the COM-pulling (incase of protein ligand complex) do we need to position restrain the ligand using genrestr and then add the topology to the topol.top file. If not why should not we restrain the ligand. Thanks in advance The initial equilibration can be approached in a number of ways that includes restraining both the protein and ligand or one or the other. Restraints are only intended to avoid large structural changes due to reorganization of the solvent. Thus you may choose to restrain the whole complex initially and then reduce or remove the restraints over the course of further equilibration. There are no hard and fast rules. Look into the literature and see what others recommend, and evaluate for yourself whether or not such a protocol is reasonable in your case. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints in SMD
Hi all, It may be naive but I would like to get some clear explanation in SMD ( COM pulling) reg. The question is, Before performing the COM-pulling (incase of protein ligand complex) do we need to position restrain the ligand using genrestr and then add the topology to the topol.top file. If not why should not we restrain the ligand. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/position-restraints-in-SMD-tp4999444.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
