Re: [gmx-users] PBC after energy minimization
On 5/1/20 9:29 AM, John Whittaker wrote: Hi Mohamed, Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve this problem after the energy minimization but I don't have .xtc file to use it as I do at the end. How can I solve this problem after the energy minimization ? You're saying that your energy minimization does not produce a trajectory (a .trr or .xtc file)? If that's the case, you just have to instruct GROMACS to periodically write to a trajectory file using options in the .mdp file (namely, nstxout). Take a look at: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html Under the section "output control" you will find what you are looking for. "Trajectories" from energy minimization are generally unreadable as the interval of saved frames is uneven. During EM, a frame is only written when the energy goes down, which is not necessarily every possible frame. I also seem to recall that there is never XTC output from EM, even if requested, because it's rather pointless. Maybe that has changed. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC after energy minimization
Hi Mohamed, > Hello everybody, > > In order to solve the PBC at the end I use the command: > > *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * > > followed by: > > *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* > > > I want to solve this problem after the energy minimization but I don't > have > .xtc file to use it as I do at the end. > > How can I solve this problem after the energy minimization ? You're saying that your energy minimization does not produce a trajectory (a .trr or .xtc file)? If that's the case, you just have to instruct GROMACS to periodically write to a trajectory file using options in the .mdp file (namely, nstxout). Take a look at: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html Under the section "output control" you will find what you are looking for. - John > > Thanks, > Mohamed > -- > 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. > John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Universität Berlin +49 0160 936 04221 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC after energy minimization
Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve this problem after the energy minimization but I don't have .xtc file to use it as I do at the end. How can I solve this problem after the energy minimization ? Thanks, Mohamed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD
On 11/28/19 11:04 AM, Ramon Crehuet wrote: Dear Justin, Thanks for your suggestion. It works, as long as I set a tpr file in the -s option. So this works: gmx trjconv -f md.trr -s md.tpr -pbc mol -center -o whole.xtc But the following does not work (where whole_center.gro is a system without water molecules with a whole centered protein and some ions): gmx trjconv -f md.xtc -s whole_center.gro -pbc mol -center -o whole.xtc I understand that this is what this warning explains: WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. This would seem anecdotal, but the problem is that I saved only the non-water system in the md.xtc. Therefore the first line works if I select to output only the protein atoms, but it gives the following error if I want the non-water atoms as output (protein + ions, all that is in the md.xtc). Fatal error: Index[413] 36378 is larger than the number of atoms in the trajectory file (433). There is a mismatch in the contents of your -f, -s and/or -n files. Again, this makes sense, as the ions are stored after the water molecules.But I am stuck with this two options. So my question is whether is there is a way to use the tpr for a xtc trajectory that contains fewer atoms than the ones defined in the tpr? Or another workaround? Use convert-tpr to make a new .tpr file that matches the contents of the .xtc file. -Justin Thanks, Ramon On 11/28/19 9:44 AM, Ramon Crehuet wrote: Dear all, As a follow-up to my question, I have seen that in a regular MD, the coordinates of the original trajectory are always smaller than the unitcell vectors, whereas this is not true in the trajectory from the replica exchange (deviations up to 1.5%). Could this be confusing trajconv? Could it be that in an exchange attempt only the coordinates of the atoms are exchanged between temperatures but not the box size? (the dynamics use a Parrinello-Rahman barostat). The entire state is exchanged (at least in the current version of the code that I'm looking at), so the box and everything else gets swapped. For a simple system of solute in water, you should be able to just do trjconv -pbc mol -center without all the intermediate steps (-pbc whole, -pbc nojump, etc). I suspect -pbc nojump won't work because you do not have a continuous trajectory during REMD, so the coordinates may change quite dramatically between snapshots, leading to a breakdown in the algorithm. -Justin Thanks again. All the best, Ramon - On 28 Nov, 2019, at 11:49, Ramon Crehuet < ramon.crehuet at iqac.csic.es > wrote: Dear all, I have run a temperature replica exchange and I would like to analyze the resulting trajectory for a given temperature (i.e. not following a replica across temperatures using demux.pl). The simulations consist of a single protein chain. I can easily generate have a whole molecule, named `whole.pdb`. When I was running regular MD, the following worked fine to generate whole structures that diffused out of the box: gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc But repeating that for one of the md.xtc of the replica exchange does not work. Each atom diffuses or of the box (i.e. without jumps) but to different directions, resulting in an apparently exploding molecule. Should there be a different treatment of RE simulations? If so, what should I do? (I have tried the -pbc nojump step followed or preceded by -pbc whole without success). Thanks for your attention. Best, Ramon -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD
Dear Justin, Thanks for your suggestion. It works, as long as I set a tpr file in the -s option. So this works: gmx trjconv -f md.trr -s md.tpr -pbc mol -center -o whole.xtc But the following does not work (where whole_center.gro is a system without water molecules with a whole centered protein and some ions): gmx trjconv -f md.xtc -s whole_center.gro -pbc mol -center -o whole.xtc I understand that this is what this warning explains: WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. This would seem anecdotal, but the problem is that I saved only the non-water system in the md.xtc. Therefore the first line works if I select to output only the protein atoms, but it gives the following error if I want the non-water atoms as output (protein + ions, all that is in the md.xtc). Fatal error: Index[413] 36378 is larger than the number of atoms in the trajectory file (433). There is a mismatch in the contents of your -f, -s and/or -n files. Again, this makes sense, as the ions are stored after the water molecules.But I am stuck with this two options. So my question is whether is there is a way to use the tpr for a xtc trajectory that contains fewer atoms than the ones defined in the tpr? Or another workaround? Thanks, Ramon On 11/28/19 9:44 AM, Ramon Crehuet wrote: > Dear all, > As a follow-up to my question, I have seen that in a regular MD, the > coordinates of the original trajectory are always smaller than the unitcell > vectors, whereas this is not true in the trajectory from the replica exchange > (deviations up to 1.5%). Could this be confusing trajconv? > Could it be that in an exchange attempt only the coordinates of the atoms are > exchanged between temperatures but not the box size? (the dynamics use a > Parrinello-Rahman barostat). The entire state is exchanged (at least in the current version of the code that I'm looking at), so the box and everything else gets swapped. For a simple system of solute in water, you should be able to just do trjconv -pbc mol -center without all the intermediate steps (-pbc whole, -pbc nojump, etc). I suspect -pbc nojump won't work because you do not have a continuous trajectory during REMD, so the coordinates may change quite dramatically between snapshots, leading to a breakdown in the algorithm. -Justin > Thanks again. > All the best, > Ramon > > - On 28 Nov, 2019, at 11:49, Ramon Crehuet < ramon.crehuet at > iqac.csic.es > wrote: > >> Dear all, >> I have run a temperature replica exchange and I would like to analyze the >> resulting trajectory for a given temperature (i.e. not following a replica >> across temperatures using demux.pl). >> The simulations consist of a single protein chain. I can easily generate >> have a >> whole molecule, named `whole.pdb`. >> When I was running regular MD, the following worked fine to generate whole >> structures that diffused out of the box: >> gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc >> But repeating that for one of the md.xtc of the replica exchange does not >> work. >> Each atom diffuses or of the box (i.e. without jumps) but to different >> directions, resulting in an apparently exploding molecule. >> Should there be a different treatment of RE simulations? If so, what should I >> do? (I have tried the -pbc nojump step followed or preceded by -pbc whole >> without success). >> Thanks for your attention. >> Best, >> Ramon -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD
On 11/28/19 9:44 AM, Ramon Crehuet wrote: Dear all, As a follow-up to my question, I have seen that in a regular MD, the coordinates of the original trajectory are always smaller than the unitcell vectors, whereas this is not true in the trajectory from the replica exchange (deviations up to 1.5%). Could this be confusing trajconv? Could it be that in an exchange attempt only the coordinates of the atoms are exchanged between temperatures but not the box size? (the dynamics use a Parrinello-Rahman barostat). The entire state is exchanged (at least in the current version of the code that I'm looking at), so the box and everything else gets swapped. For a simple system of solute in water, you should be able to just do trjconv -pbc mol -center without all the intermediate steps (-pbc whole, -pbc nojump, etc). I suspect -pbc nojump won't work because you do not have a continuous trajectory during REMD, so the coordinates may change quite dramatically between snapshots, leading to a breakdown in the algorithm. -Justin Thanks again. All the best, Ramon - On 28 Nov, 2019, at 11:49, Ramon Crehuet wrote: Dear all, I have run a temperature replica exchange and I would like to analyze the resulting trajectory for a given temperature (i.e. not following a replica across temperatures using demux.pl). The simulations consist of a single protein chain. I can easily generate have a whole molecule, named `whole.pdb`. When I was running regular MD, the following worked fine to generate whole structures that diffused out of the box: gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc But repeating that for one of the md.xtc of the replica exchange does not work. Each atom diffuses or of the box (i.e. without jumps) but to different directions, resulting in an apparently exploding molecule. Should there be a different treatment of RE simulations? If so, what should I do? (I have tried the -pbc nojump step followed or preceded by -pbc whole without success). Thanks for your attention. Best, Ramon -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD
Dear all, As a follow-up to my question, I have seen that in a regular MD, the coordinates of the original trajectory are always smaller than the unitcell vectors, whereas this is not true in the trajectory from the replica exchange (deviations up to 1.5%). Could this be confusing trajconv? Could it be that in an exchange attempt only the coordinates of the atoms are exchanged between temperatures but not the box size? (the dynamics use a Parrinello-Rahman barostat). Thanks again. All the best, Ramon - On 28 Nov, 2019, at 11:49, Ramon Crehuet wrote: > Dear all, > I have run a temperature replica exchange and I would like to analyze the > resulting trajectory for a given temperature (i.e. not following a replica > across temperatures using demux.pl). > The simulations consist of a single protein chain. I can easily generate have > a > whole molecule, named `whole.pdb`. > When I was running regular MD, the following worked fine to generate whole > structures that diffused out of the box: > gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc > But repeating that for one of the md.xtc of the replica exchange does not > work. > Each atom diffuses or of the box (i.e. without jumps) but to different > directions, resulting in an apparently exploding molecule. > Should there be a different treatment of RE simulations? If so, what should I > do? (I have tried the -pbc nojump step followed or preceded by -pbc whole > without success). > Thanks for your attention. > Best, > Ramon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD
Dear all, I have run a temperature replica exchange and I would like to analyze the resulting trajectory for a given temperature (i.e. not following a replica across temperatures using demux.pl). The simulations consist of a single protein chain. I can easily generate have a whole molecule, named `whole.pdb`. When I was running regular MD, the following worked fine to generate whole structures that diffused out of the box: gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc But repeating that for one of the md.xtc of the replica exchange does not work. Each atom diffuses or of the box (i.e. without jumps) but to different directions, resulting in an apparently exploding molecule. Should there be a different treatment of RE simulations? If so, what should I do? (I have tried the -pbc nojump step followed or preceded by -pbc whole without success). Thanks for your attention. Best, Ramon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC conditions for Vacuum simulation
Hi, No. Models without cutoffs will scale badly with particle count. Adding cutoffs is not always a performance win either, because while that saves computation of interactions, it adds the need to periodically search for which particle interactions to compute. Mark On Sat., 9 Feb. 2019, 17:24 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I am trying to model a peptide in gas phase which requires proper > conditions like: no PBC, no cut-offs for VanderWaals and electrostatics, > coulomb type not PME. However, this increases computational time by N^2 for > N number of atoms. Is there a way to mitigate this? > > Many thanks, > Neena > > -- > 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] PBC conditions for Vacuum simulation
Hello gromacs users, I am trying to model a peptide in gas phase which requires proper conditions like: no PBC, no cut-offs for VanderWaals and electrostatics, coulomb type not PME. However, this increases computational time by N^2 for N number of atoms. Is there a way to mitigate this? Many thanks, Neena -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC for ewald-geometry 3dc warning
Hi everyone, I am trying to simulate a crystal slab using 3dc Ewald correction and PBC in xyz with dimensions 3.5nm*4.4nm*3.2nm and with the box length of more than 3xZ in the z-direction with my slab in the center of the box, as recommended in GROMACS manual. I am getting the following warning: "With PME and ewald_geometry = 3dc you should use pbc = xy" I looked at different mail list I could find on internet listed below: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-June/113997.html https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg27043.html https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-February/118464.html I couldn't find any justification of why we need to used pbc in xy direction and how it will take care of periodicity in z-direction which was used in the original paper https://aip.scitation.org/doi/10.1063/1.479595. I also want to know if I can ignore this warning and what could be the repercussions of ignoring this warning? I have already tried using the 2018 version of GROMACS as suggested in one of the mail lists but warning persist. Thanks! Lakshman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC fix for visualization
Hi Dallas and other Gromacs users, I used -pbc whole and -ur compact in the first step "System" index group And then, used the output file for -pbc cluster. Choosing the "System" index for clustering gave the best result I got. (Although there are still few lipids which are not completely in the places they should be). Anyway, the outputs are reasonable. However, I have ca. 100 simulation systems each of ca. 500 ns. (each system composed of ca. 4000 molecules) Doing this clustering on the whole system takes a considerable time. I thought I might be able to do the clustering on a group of atoms (an index group composed of P in lipids and O in water molecules). This, however, did not work and gmx trjconv complained about: "Molecule 1 marked for clustering but not atom 1 in it - check your index!" I was wondering what would be your solution to this? Cheers, Mohsen On Mon, May 22, 2017 at 11:45 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Dallas, > > Thanks for your reply. > I did try -pbc cluster for waters. It could fix it somehow but not > completely. > After that, I had to use -pbc center to fix it. Still, I do not get what I > want. > Unfortunately, some waters and lipids are appearing from the other side of > the box. > > Cheers, > Mohsen > > > On Sun, May 21, 2017 at 8:12 PM, Dallas Warren > wrote: > >> I have found the cluster option of -pbc to work well for putting >> aggregates back together correctly. Some times you do need an index >> file and appropriate groups to assist with it getting it right. >> >> gmx trjconv -pbc cluster >> Catch ya, >> >> Dr. Dallas Warren >> Drug Delivery, Disposition and Dynamics >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3052 >> dallas.war...@monash.edu >> - >> When the only tool you own is a hammer, every problem begins to resemble >> a nail. >> >> >> On 16 May 2017 at 07:50, Mohsen Ramezanpour >> wrote: >> > Dear Gromacs users, >> > >> > I have an HII phase made of one inverted cylinder (and waters inside) >> in a >> > triclinic box with 90, 90, 60 angles. After running the simulation, this >> > cylinder become bent like a curve. I.e. is not a perfect cylinder >> anymore. >> > As a result, some water molecules and lipids pass the box sides and >> enter >> > from the other side of box because of PBC. >> > Now, I want to make the cylinder again but I am not sure how to do so. >> > >> > The best I could do was to use "-pbc mol -ur compact" options in >> trjconv. >> > However, here are still some lipids and molecules which are not part of >> the >> > cylinder. >> > >> > Any idea how could I fix the effect of these PBC in visualization? >> > >> > Thanks >> > Mohsen >> > >> > -- >> > *Rewards work better than punishment ...* >> > -- >> > 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. >> > > > > -- > *Rewards work better than punishment ...* > -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problems related to comm-grps in membrane simulation?
Hi, I'm having difficulty with a membrane receptor simulation. It seems like whenever the receptor crosses the boundary (I'm using PBC), the box gets distorted so that the z axis is compressed from 10.2nm to 8-8.2nm which is too large a change. I was initially using System for the comm-grps option in my mdp file, later thinking that this might be the problem I switched to an option that separates membrane from solution. This seems to have helped, but I do not understand why it would. What does this have to do with the receptor crossing the boundary? I'd really appreciate some insight. Here's my original mdp file: ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/roe include = ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.004 nsteps = 2 ; For exact run continuation or redoing part of a run init-step= 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation-part = 1 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= System ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld_seed = -1 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax-shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 2500 nstcalcenergy= 100 nstenergy= 2500 ; Output frequency and precision for .xtc file nstxout-compressed = 2500 compressed-x-precision = 1000 ; This selects the subset of atoms for the compressed ; trajectory file. You can select multiple groups. By ; default, all atoms will be written. compressed-x-grps= ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) cutoff-scheme= Verlet ; nblist update frequency nstlist = 20 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic-molecules = no ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, ; a value of -1 means: use rlist verlet-buffer-tolerance = 0.005 ; nblist cut-off rlist= 1.2 ; long-range cut-off for switched potentials rlistlong= 1.4 nstcalclr= -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME coulomb-modifier = Potential-shift-Verlet rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 1 epsilon-rf = 0 ; Method for doing Van der Waals vdw-type = Cut-off vdw-modifier = force-switch ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Separate tables between energy group pairs energygrp-table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 ; FFT grid size, when a value is 0 fourierspacing will be used fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald-rtol = 1e-05 ewald-rtol-lj= 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 ; IMPLICIT SOLVENT ALGORITHM implicit-solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb-algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii
Re: [gmx-users] PBC
On 2/12/18 8:44 AM, Ahmed Mashaly wrote: Hi If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference? This is because the protein has jumped after em step, and if I have to use md.tpr as reference for md.xtc, I will have to recenter it after every step of em, nvt, npt You can use whatever reference coordinates you want. Energy minimization generally shouldn't result in large structural changes, so make sure you have a sufficiently large box to avoid spurious minimum image interactions. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC
Hi If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference? This is because the protein has jumped after em step, and if I have to use md.tpr as reference for md.xtc, I will have to recenter it after every step of em, nvt, npt Kind Regards,Ahmed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pbc
On 8/16/17 4:24 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gromacs users I need to visualize my md_0_1.tpr , so i issued trjconv -s md_0_1.tpr -f md_0_1.xtc -o xxx.pdb -pbc nojump -dt 10to remove the jumps over the boundaries and make a continuous trajectoryPBCBut when i visualized my complex by pymol, the protein appeared broken . Would you please help me to solve it? The molecules are broken because you didn't tell trjconv to make them whole. Google is your friend... http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Pbc
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gromacs users I need to visualize my md_0_1.tpr , so i issued trjconv -s md_0_1.tpr -f md_0_1.xtc -o xxx.pdb -pbc nojump -dt 10to remove the jumps over the boundaries and make a continuous trajectoryPBCBut when i visualized my complex by pymol, the protein appeared broken . Would you please help me to solve it? BestFarial Sent from Yahoo Mail for iPhone -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC ISSUES IN GROMACS
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions had useful information Mark On Mon, 14 Aug 2017 09:17 Neha Gupta wrote: > Hi gromacs users, > > After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc > > However, in the movie file, I witnessed bizarre long bonds... > > How to fix it? > > Any suggestions please? > > > Thanks, > Neha > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC ISSUES IN GROMACS
On 14/08/17 09:17, Neha Gupta wrote: Hi gromacs users, After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc However, in the movie file, I witnessed bizarre long bonds... How to fix it? Any suggestions please? trjconv -pbc whole Thanks, Neha -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC ISSUES IN GROMACS
Hi gromacs users, After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc However, in the movie file, I witnessed bizarre long bonds... How to fix it? Any suggestions please? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC fix for visualization
Hi Dallas, Thanks for your reply. I did try -pbc cluster for waters. It could fix it somehow but not completely. After that, I had to use -pbc center to fix it. Still, I do not get what I want. Unfortunately, some waters and lipids are appearing from the other side of the box. Cheers, Mohsen On Sun, May 21, 2017 at 8:12 PM, Dallas Warren wrote: > I have found the cluster option of -pbc to work well for putting > aggregates back together correctly. Some times you do need an index > file and appropriate groups to assist with it getting it right. > > gmx trjconv -pbc cluster > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 16 May 2017 at 07:50, Mohsen Ramezanpour > wrote: > > Dear Gromacs users, > > > > I have an HII phase made of one inverted cylinder (and waters inside) in > a > > triclinic box with 90, 90, 60 angles. After running the simulation, this > > cylinder become bent like a curve. I.e. is not a perfect cylinder > anymore. > > As a result, some water molecules and lipids pass the box sides and enter > > from the other side of box because of PBC. > > Now, I want to make the cylinder again but I am not sure how to do so. > > > > The best I could do was to use "-pbc mol -ur compact" options in > trjconv. > > However, here are still some lipids and molecules which are not part of > the > > cylinder. > > > > Any idea how could I fix the effect of these PBC in visualization? > > > > Thanks > > Mohsen > > > > -- > > *Rewards work better than punishment ...* > > -- > > 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. > -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC fix for visualization
I have found the cluster option of -pbc to work well for putting aggregates back together correctly. Some times you do need an index file and appropriate groups to assist with it getting it right. gmx trjconv -pbc cluster Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 16 May 2017 at 07:50, Mohsen Ramezanpour wrote: > Dear Gromacs users, > > I have an HII phase made of one inverted cylinder (and waters inside) in a > triclinic box with 90, 90, 60 angles. After running the simulation, this > cylinder become bent like a curve. I.e. is not a perfect cylinder anymore. > As a result, some water molecules and lipids pass the box sides and enter > from the other side of box because of PBC. > Now, I want to make the cylinder again but I am not sure how to do so. > > The best I could do was to use "-pbc mol -ur compact" options in trjconv. > However, here are still some lipids and molecules which are not part of the > cylinder. > > Any idea how could I fix the effect of these PBC in visualization? > > Thanks > Mohsen > > -- > *Rewards work better than punishment ...* > -- > 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] PBC fix for visualization
Dear Gromacs users, I have an HII phase made of one inverted cylinder (and waters inside) in a triclinic box with 90, 90, 60 angles. After running the simulation, this cylinder become bent like a curve. I.e. is not a perfect cylinder anymore. As a result, some water molecules and lipids pass the box sides and enter from the other side of box because of PBC. Now, I want to make the cylinder again but I am not sure how to do so. The best I could do was to use "-pbc mol -ur compact" options in trjconv. However, here are still some lipids and molecules which are not part of the cylinder. Any idea how could I fix the effect of these PBC in visualization? Thanks Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
On 5/5/17 1:37 PM, Alex wrote: Dear Gromacs user, I want to study the interaction between a nanoparticle(5 nm diameter) and some heptapeptide around the nanoparticle in aqueous solution. I put the nanoparticle in the center of a box and the rest are around it. I was wondering if I should use PBC (periodic boundary condition) in such a system? What is the advantage of the using PBC here? The same as any system - you don't have boundary effects and your system won't turn into a quickly evaporating droplet. -Justin The disadvantage of using PBC here is that a very big box should be used to avoid interaction between a peptide and another peptide in the adjacent cell. Regards, Alex -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC
Dear Gromacs user, I want to study the interaction between a nanoparticle(5 nm diameter) and some heptapeptide around the nanoparticle in aqueous solution. I put the nanoparticle in the center of a box and the rest are around it. I was wondering if I should use PBC (periodic boundary condition) in such a system? What is the advantage of the using PBC here? The disadvantage of using PBC here is that a very big box should be used to avoid interaction between a peptide and another peptide in the adjacent cell. Regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem
Hello, I try to visualize a .gro file from Martini simulation. However, I noticed that the lipids always above the water molecule and my protein split into two. Even after I run the following command: gmx trjconv -s dppc-md.tpr -f dppc-md.gro -pbc whole -dump 0 -o dppc-md-pbc.gro The issue is still there. Here is a snapshot for my problem: https://www.dropbox.com/s/qvoxa70tr625w46/pbc.jpg?dl=0 Does anybody have any idea how to solve this problem? Thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC issues with membrane-peptide simulation
Dear users, Well, I have found another solution for avoiding the diffusion through the periodic boundary in such simulations. Hope this is helpful to others doing similar work. Basically, the idea is to apply a biasing potential to the COM of the peptides to pull them towards the membrane so as to ensure interaction with the lipid bilayer. Thereafter, normal production simulations can be performed on the peptide membrane complex. See the following paper: Li, J., Liu, S., Lakshminarayanan, R., Bai, Y., Pervushin, K., Verma, C., and Beuerman, R.W. (2013). Molecular simulations suggest how a branched antimicrobial peptide perturbs a bacterial membrane and enhances permeability. Biochim. Biophys. Acta *1828*, 1112–1121. Best Regards, Abhishek Acharya On Thu, Nov 10, 2016 at 12:48 PM, Abhi Acharya wrote: > Sorry for that Mark. > > Basically, our experimental studies show that our designed peptides (2-3 > different peptides) are involved in membrane destabilization but their > activity (in terms of MIC values) varies. We want to understand the > molecular underpinnings of the membrane destabilization process and > possibly explain the variation in activities of the peptides. Therefore, we > wanted to perform some simulations starting from the point where some > amount of peptides are randomly added to the simulation box on one side of > the membrane (about 5 nm away from the upper leaflet) and see how the > system evolves. > > The problem is that some of the peptides diffuse along the z-direction > such that they exit the simulation box and appear on the other side near to > the lower leaflet. > > Hope this is helpful. > > Thanks and Regards, > Abhishek Acharya > > > > > > On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham > wrote: > >> Hi, >> >> You haven't said what you're trying to model, so it's going to be hard for >> someone to help out :-) >> >> Mark >> >> On Thu, 10 Nov 2016 05:21 Abhi Acharya wrote: >> >> > Thank you Stephane for your suggestion. Though this seems like a nice >> > solution to circumvent the problem, but do you think this is the normal >> way >> > to go about it? I have never found anyone reporting such a methodology >> for >> > membrane peptide simulation. Also, I can anticipate significant >> increase in >> > computational costs for a double bilayer system. I have a 800 lipid >> > molecules in a single bilayer, so this is significant factor for me. >> > >> > Thanks and Regards, >> > Abhishek >> > >> > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 < >> stephane.a...@cea.fr >> > > >> > wrote: >> > >> > > Hi, >> > > >> > > it is not an issue !! To resolve your problem you could simulate two >> > > bilayer in box and insert the peptides between them. >> > > >> > > HTH >> > > >> > > -- >> > > >> > > Message: 6 >> > > Date: Wed, 9 Nov 2016 16:07:26 +0530 >> > > From: Abhi Acharya >> > > To: gromacs.org_gmx-users@maillist.sys.kth.se >> > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation >> > > Message-ID: >> > > > > > gmail.com> >> > > Content-Type: text/plain; charset=UTF-8 >> > > >> > > Dear Gromacs users, >> > > >> > > I am trying to simulate a system consisting of a lipid bilayer and few >> > > peptides. The peptides have been added randomly to the simulation box >> > only >> > > on one side of the membrane. I ran a 100 ns simulation of the system >> > using >> > > CHARMM36 forcefeild. However, I find that within the first few ns, >> some >> > of >> > > the peptides appear on the other side of the membrane. I think that >> this >> > is >> > > because of the diffusion of the peptides though the periodic boundary. >> > > Kindly suggest how to tackle this problem. I have used COM motion >> > removal >> > > on the whole system for the said simulation. >> > > >> > > Regards, >> > > Abhishek Acharya >> > > >> > > >> > > -- >> > > >> > > -- >> > > 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. >> > > >> > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32 >> > > ** >> > > -- >> > > 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 >> >
Re: [gmx-users] PBC issues with membrane-peptide simulation
Sorry for that Mark. Basically, our experimental studies show that our designed peptides (2-3 different peptides) are involved in membrane destabilization but their activity (in terms of MIC values) varies. We want to understand the molecular underpinnings of the membrane destabilization process and possibly explain the variation in activities of the peptides. Therefore, we wanted to perform some simulations starting from the point where some amount of peptides are randomly added to the simulation box on one side of the membrane (about 5 nm away from the upper leaflet) and see how the system evolves. The problem is that some of the peptides diffuse along the z-direction such that they exit the simulation box and appear on the other side near to the lower leaflet. Hope this is helpful. Thanks and Regards, Abhishek Acharya On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham wrote: > Hi, > > You haven't said what you're trying to model, so it's going to be hard for > someone to help out :-) > > Mark > > On Thu, 10 Nov 2016 05:21 Abhi Acharya wrote: > > > Thank you Stephane for your suggestion. Though this seems like a nice > > solution to circumvent the problem, but do you think this is the normal > way > > to go about it? I have never found anyone reporting such a methodology > for > > membrane peptide simulation. Also, I can anticipate significant increase > in > > computational costs for a double bilayer system. I have a 800 lipid > > molecules in a single bilayer, so this is significant factor for me. > > > > Thanks and Regards, > > Abhishek > > > > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 < > stephane.a...@cea.fr > > > > > wrote: > > > > > Hi, > > > > > > it is not an issue !! To resolve your problem you could simulate two > > > bilayer in box and insert the peptides between them. > > > > > > HTH > > > > > > -- > > > > > > Message: 6 > > > Date: Wed, 9 Nov 2016 16:07:26 +0530 > > > From: Abhi Acharya > > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation > > > Message-ID: > > > > > gmail.com> > > > Content-Type: text/plain; charset=UTF-8 > > > > > > Dear Gromacs users, > > > > > > I am trying to simulate a system consisting of a lipid bilayer and few > > > peptides. The peptides have been added randomly to the simulation box > > only > > > on one side of the membrane. I ran a 100 ns simulation of the system > > using > > > CHARMM36 forcefeild. However, I find that within the first few ns, some > > of > > > the peptides appear on the other side of the membrane. I think that > this > > is > > > because of the diffusion of the peptides though the periodic boundary. > > > Kindly suggest how to tackle this problem. I have used COM motion > > removal > > > on the whole system for the said simulation. > > > > > > Regards, > > > Abhishek Acharya > > > > > > > > > -- > > > > > > -- > > > 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. > > > > > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32 > > > ** > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/
Re: [gmx-users] PBC issues with membrane-peptide simulation
Hi, You haven't said what you're trying to model, so it's going to be hard for someone to help out :-) Mark On Thu, 10 Nov 2016 05:21 Abhi Acharya wrote: > Thank you Stephane for your suggestion. Though this seems like a nice > solution to circumvent the problem, but do you think this is the normal way > to go about it? I have never found anyone reporting such a methodology for > membrane peptide simulation. Also, I can anticipate significant increase in > computational costs for a double bilayer system. I have a 800 lipid > molecules in a single bilayer, so this is significant factor for me. > > Thanks and Regards, > Abhishek > > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 > > wrote: > > > Hi, > > > > it is not an issue !! To resolve your problem you could simulate two > > bilayer in box and insert the peptides between them. > > > > HTH > > > > -- > > > > Message: 6 > > Date: Wed, 9 Nov 2016 16:07:26 +0530 > > From: Abhi Acharya > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation > > Message-ID: > > > gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Dear Gromacs users, > > > > I am trying to simulate a system consisting of a lipid bilayer and few > > peptides. The peptides have been added randomly to the simulation box > only > > on one side of the membrane. I ran a 100 ns simulation of the system > using > > CHARMM36 forcefeild. However, I find that within the first few ns, some > of > > the peptides appear on the other side of the membrane. I think that this > is > > because of the diffusion of the peptides though the periodic boundary. > > Kindly suggest how to tackle this problem. I have used COM motion > removal > > on the whole system for the said simulation. > > > > Regards, > > Abhishek Acharya > > > > > > -- > > > > -- > > 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. > > > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32 > > ** > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC issues with membrane-peptide simulation
Thank you Stephane for your suggestion. Though this seems like a nice solution to circumvent the problem, but do you think this is the normal way to go about it? I have never found anyone reporting such a methodology for membrane peptide simulation. Also, I can anticipate significant increase in computational costs for a double bilayer system. I have a 800 lipid molecules in a single bilayer, so this is significant factor for me. Thanks and Regards, Abhishek On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 wrote: > Hi, > > it is not an issue !! To resolve your problem you could simulate two > bilayer in box and insert the peptides between them. > > HTH > > -- > > Message: 6 > Date: Wed, 9 Nov 2016 16:07:26 +0530 > From: Abhi Acharya > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation > Message-ID: > gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Gromacs users, > > I am trying to simulate a system consisting of a lipid bilayer and few > peptides. The peptides have been added randomly to the simulation box only > on one side of the membrane. I ran a 100 ns simulation of the system using > CHARMM36 forcefeild. However, I find that within the first few ns, some of > the peptides appear on the other side of the membrane. I think that this is > because of the diffusion of the peptides though the periodic boundary. > Kindly suggest how to tackle this problem. I have used COM motion removal > on the whole system for the said simulation. > > Regards, > Abhishek Acharya > > > -- > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32 > ** > -- > 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] PBC issues with membrane-peptide simulation
Hi, it is not an issue !! To resolve your problem you could simulate two bilayer in box and insert the peptides between them. HTH -- Message: 6 Date: Wed, 9 Nov 2016 16:07:26 +0530 From: Abhi Acharya To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation Message-ID: Content-Type: text/plain; charset=UTF-8 Dear Gromacs users, I am trying to simulate a system consisting of a lipid bilayer and few peptides. The peptides have been added randomly to the simulation box only on one side of the membrane. I ran a 100 ns simulation of the system using CHARMM36 forcefeild. However, I find that within the first few ns, some of the peptides appear on the other side of the membrane. I think that this is because of the diffusion of the peptides though the periodic boundary. Kindly suggest how to tackle this problem. I have used COM motion removal on the whole system for the said simulation. Regards, Abhishek Acharya -- -- 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. End of gromacs.org_gmx-users Digest, Vol 151, Issue 32 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -pbc nojump failure
Dear Irem, You may want to run the trajectory through trjconv and translate it, or use e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of trial and error. Kind regards, Erik > On 31 Mar 2016, at 18:36, Irem Altan wrote: > > I think the problem is that I can’t seem to start from an unfragmented > structure. I start from the .pdb file, where the protein is a whole, and end > up with a .tpr file that is fragmented. The interesting thing is, this did > not happen with version 4.6.5 (I now use 5.1.2). Do I have to do something > extra while preparing the simulation system? > > Here is what I’m currently doing: > > gmx pdb2gmx -f .pdb -o box.gro -p topol.top (then I choose > amber99sb and tip4pew) > gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro > gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top > gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05 (I > choose to replace the solvation waters, SOL) > gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr > gmx mdrun -v -deffnm em > gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr > > Then I run the simulation with mdrun. The .mdp files are almost identical to > Justin’s files from the Lysozyme tutorial. In the above steps, is there > something that seems like it could cause the fragmentation issue? > > Best, > Irem > >> On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar wrote: >> >> No! You can't do that, because fitting will cause the PBC and the >> coordinates to mismatch. So 'nojump' after that will for sure screw up the >> coordinates. Check the trjconv workflow on the Gromacs site. >> >> Cheers, >> >> Tsjerk >> On Mar 31, 2016 14:23, "Francesco Carbone" wrote: >> >>> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) >>> later. >>> >>> Cheers, >>> >>> Fra >>> >>> On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: >>> Hi Irem, Check the structure in nvt_water_frozen.tpr: gmx editconf -f nvt_water_frozen.tpr -o ref.pdb Cheers, Tsjerk On Mar 31, 2016 00:04, "Irem Altan" wrote: > Hi, > > I am simulating a protein in its unit cell. I use the original .pdb >>> file > as an input, so the initial molecule is not fragmented. At the end of >>> the > simulation, I generate a .pdb file containing the trajectory of the protein > as follows: > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > nojump -o prot.pdb > > Despite the fact that I use -pbc nojump, I still get all the >>> coordinates > wrapped into the unit cell, and therefore the protein fragmented. What > could be wrong? (I use GROMACS 5.1.2) > > Best, > Irem > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > 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.
Re: [gmx-users] -pbc nojump failure
I think the problem is that I can’t seem to start from an unfragmented structure. I start from the .pdb file, where the protein is a whole, and end up with a .tpr file that is fragmented. The interesting thing is, this did not happen with version 4.6.5 (I now use 5.1.2). Do I have to do something extra while preparing the simulation system? Here is what I’m currently doing: gmx pdb2gmx -f .pdb -o box.gro -p topol.top (then I choose amber99sb and tip4pew) gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05 (I choose to replace the solvation waters, SOL) gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr Then I run the simulation with mdrun. The .mdp files are almost identical to Justin’s files from the Lysozyme tutorial. In the above steps, is there something that seems like it could cause the fragmentation issue? Best, Irem > On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar wrote: > > No! You can't do that, because fitting will cause the PBC and the > coordinates to mismatch. So 'nojump' after that will for sure screw up the > coordinates. Check the trjconv workflow on the Gromacs site. > > Cheers, > > Tsjerk > On Mar 31, 2016 14:23, "Francesco Carbone" wrote: > >> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) >> later. >> >> Cheers, >> >> Fra >> >> On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: >> >>> Hi Irem, >>> >>> Check the structure in nvt_water_frozen.tpr: >>> >>> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb >>> >>> Cheers, >>> >>> Tsjerk >>> On Mar 31, 2016 00:04, "Irem Altan" wrote: >>> Hi, I am simulating a protein in its unit cell. I use the original .pdb >> file as an input, so the initial molecule is not fragmented. At the end of >> the simulation, I generate a .pdb file containing the trajectory of the >>> protein as follows: gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc nojump -o prot.pdb Despite the fact that I use -pbc nojump, I still get all the >> coordinates wrapped into the unit cell, and therefore the protein fragmented. What could be wrong? (I use GROMACS 5.1.2) Best, Irem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -pbc nojump failure
No! You can't do that, because fitting will cause the PBC and the coordinates to mismatch. So 'nojump' after that will for sure screw up the coordinates. Check the trjconv workflow on the Gromacs site. Cheers, Tsjerk On Mar 31, 2016 14:23, "Francesco Carbone" wrote: > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) > later. > > Cheers, > > Fra > > On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > > > Hi Irem, > > > > Check the structure in nvt_water_frozen.tpr: > > > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > > > Cheers, > > > > Tsjerk > > On Mar 31, 2016 00:04, "Irem Altan" wrote: > > > > > Hi, > > > > > > I am simulating a protein in its unit cell. I use the original .pdb > file > > > as an input, so the initial molecule is not fragmented. At the end of > the > > > simulation, I generate a .pdb file containing the trajectory of the > > protein > > > as follows: > > > > > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > > > nojump -o prot.pdb > > > > > > Despite the fact that I use -pbc nojump, I still get all the > coordinates > > > wrapped into the unit cell, and therefore the protein fragmented. What > > > could be wrong? (I use GROMACS 5.1.2) > > > > > > Best, > > > Irem > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -pbc nojump failure
Hi, Thanks. If I do that, the reference structure would be what’s in the .tpr file, right? Best, Irem > On Mar 31, 2016, at 8:22 AM, Francesco Carbone wrote: > > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. > > Cheers, > > Fra > > On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > >> Hi Irem, >> >> Check the structure in nvt_water_frozen.tpr: >> >> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb >> >> Cheers, >> >> Tsjerk >> On Mar 31, 2016 00:04, "Irem Altan" wrote: >> >>> Hi, >>> >>> I am simulating a protein in its unit cell. I use the original .pdb file >>> as an input, so the initial molecule is not fragmented. At the end of the >>> simulation, I generate a .pdb file containing the trajectory of the >> protein >>> as follows: >>> >>> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc >>> nojump -o prot.pdb >>> >>> Despite the fact that I use -pbc nojump, I still get all the coordinates >>> wrapped into the unit cell, and therefore the protein fragmented. What >>> could be wrong? (I use GROMACS 5.1.2) >>> >>> Best, >>> Irem >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -pbc nojump failure
Hi, Thanks for your suggestion. Unsurprisingly, the structure in nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb file as reference, somehow? Best, Irem > On Mar 31, 2016, at 12:45 AM, Tsjerk Wassenaar wrote: > > Hi Irem, > > Check the structure in nvt_water_frozen.tpr: > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > Cheers, > > Tsjerk > On Mar 31, 2016 00:04, "Irem Altan" wrote: > >> Hi, >> >> I am simulating a protein in its unit cell. I use the original .pdb file >> as an input, so the initial molecule is not fragmented. At the end of the >> simulation, I generate a .pdb file containing the trajectory of the protein >> as follows: >> >> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc >> nojump -o prot.pdb >> >> Despite the fact that I use -pbc nojump, I still get all the coordinates >> wrapped into the unit cell, and therefore the protein fragmented. What >> could be wrong? (I use GROMACS 5.1.2) >> >> Best, >> Irem >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -pbc nojump failure
You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. Cheers, Fra On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > Hi Irem, > > Check the structure in nvt_water_frozen.tpr: > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > Cheers, > > Tsjerk > On Mar 31, 2016 00:04, "Irem Altan" wrote: > > > Hi, > > > > I am simulating a protein in its unit cell. I use the original .pdb file > > as an input, so the initial molecule is not fragmented. At the end of the > > simulation, I generate a .pdb file containing the trajectory of the > protein > > as follows: > > > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > > nojump -o prot.pdb > > > > Despite the fact that I use -pbc nojump, I still get all the coordinates > > wrapped into the unit cell, and therefore the protein fragmented. What > > could be wrong? (I use GROMACS 5.1.2) > > > > Best, > > Irem > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -pbc nojump failure
Hi Irem, Check the structure in nvt_water_frozen.tpr: gmx editconf -f nvt_water_frozen.tpr -o ref.pdb Cheers, Tsjerk On Mar 31, 2016 00:04, "Irem Altan" wrote: > Hi, > > I am simulating a protein in its unit cell. I use the original .pdb file > as an input, so the initial molecule is not fragmented. At the end of the > simulation, I generate a .pdb file containing the trajectory of the protein > as follows: > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > nojump -o prot.pdb > > Despite the fact that I use -pbc nojump, I still get all the coordinates > wrapped into the unit cell, and therefore the protein fragmented. What > could be wrong? (I use GROMACS 5.1.2) > > Best, > Irem > -- > 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] -pbc nojump failure
Hi, I am simulating a protein in its unit cell. I use the original .pdb file as an input, so the initial molecule is not fragmented. At the end of the simulation, I generate a .pdb file containing the trajectory of the protein as follows: gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc nojump -o prot.pdb Despite the fact that I use -pbc nojump, I still get all the coordinates wrapped into the unit cell, and therefore the protein fragmented. What could be wrong? (I use GROMACS 5.1.2) Best, Irem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pbc
On 1/5/16 11:58 AM, Parvez Mh wrote: Dear all: I am using pbc in all directions, it is expected that, i will observe broken molecules in central box. But i am wondering, some molecules are out of box when i visualize with vmd. What would the right explanation of this? PBC is the explanation. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pbc
Dear all: I am using pbc in all directions, it is expected that, i will observe broken molecules in central box. But i am wondering, some molecules are out of box when i visualize with vmd. What would the right explanation of this? Regards Masrul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pbc
On 10/19/15 9:59 PM, Sana Saeed wrote: good morning gmx usersi want to visualize the box from my gro file. I am using VMD , i read the manual but couldnt understand how to use my own vectors to visualize box. actually i want to see if the atoms are out of box or inside.Thanks in advance In the VMD Tk console: pbc box If you have problems with VMD, please post to their mailing list. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pbc
good morning gmx usersi want to visualize the box from my gro file. I am using VMD , i read the manual but couldnt understand how to use my own vectors to visualize box. actually i want to see if the atoms are out of box or inside.Thanks in advance Autumn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pbc=xy with 2 walls and verlet scheme
Hi all, I use GROMACS 5.1. With pbc = xy nwall= 2 and cutoff-scheme = group everything runs fine, however, when I switch to cutoff-scheme = verlet the simulation crashes with a floating exception. Both cases can be downloaded here https://www.dropbox.com/s/0kuos2devdy5hpy/group.tar.gz?dl=0. Does anyone have an idea what might be going wrong? The issue sounds related to Bug 1660 ( http://redmine.gromacs.org/issues/1660 ) Best, Joerg -- Joerg Sauter Theory & Bio-Systems Max Planck Institute of Colloids and Interfaces Potsdam, Germany -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
I thought so :D Thanks! On Thu, Oct 8, 2015 at 9:37 AM, mah maz wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the > system is in vacuum. > There are some parameters in the .mdp file that I haven't defined and I > don't want them to be applied during simulation. However in the mdout.mdp > They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role > in the simulation? > > Thanks! > > On Mon, Oct 5, 2015 at 2:26 PM, mah maz wrote: > >> Hi Mark, >> Thanks. It seems the default is pbc =xyz. But my question is if I don't >> use PBC, can I use grid, or grid is only meaningful when PBC is defined? >> >> On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: >> >>> Dear users, >>> >>> If I dont define pbc=no, what is the default type for gromacs? Is it >>> right if I dont use pbc=no in my system while using grid for ns-type? >>> >>> 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.
Re: [gmx-users] PBC
Hi, On Thu, Oct 8, 2015 at 8:08 AM mah maz wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the system > is in vacuum. > There are some parameters in the .mdp file that I haven't defined and I > don't want them to be applied during simulation. However in the mdout.mdp > They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role > in the simulation? > Yes, gen-seed kills a kitten and ewald-rtol launches nuclear missiles ;-) (Stuff that configures inactive algorithms isn't active.) Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
Hi Mark Thank you. I suppose grid can be used without PBC specially when the system is in vacuum. There are some parameters in the .mdp file that I haven't defined and I don't want them to be applied during simulation. However in the mdout.mdp They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role in the simulation? Thanks! On Mon, Oct 5, 2015 at 2:26 PM, mah maz wrote: > Hi Mark, > Thanks. It seems the default is pbc =xyz. But my question is if I don't > use PBC, can I use grid, or grid is only meaningful when PBC is defined? > > On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > >> Dear users, >> >> If I dont define pbc=no, what is the default type for gromacs? Is it >> right if I dont use pbc=no in my system while using grid for ns-type? >> >> 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] PBC in membrane protein system
Hi all, I am simulating a membrane protein in coarse-grained mode. The protein diffuse in the membrane and in the final frame my protein is in one of the box borders, so the coordinates are splitted to the opposite border (PBC). Then when I used backward.py to translate to all-atom coordinates, also results in splitted coordinates. I've tried several trjconv option with any success. How can I get the protein centered in the membrane? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
Hi, I don't really remember. I suspect not, so I would look up the docs for ns-type, which should mention limitations, and otherwise try it out. grompp and/or mdrun are pretty good at complaining about things they can't do. Mark On Mon, Oct 5, 2015 at 12:56 PM mah maz wrote: > Hi Mark, > Thanks. It seems the default is pbc =xyz. But my question is if I don't use > PBC, can I use grid, or grid is only meaningful when PBC is defined? > > On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > > > Dear users, > > > > If I dont define pbc=no, what is the default type for gromacs? Is it > right > > if I dont use pbc=no in my system while using grid for ns-type? > > > > 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
Hi Mark, Thanks. It seems the default is pbc =xyz. But my question is if I don't use PBC, can I use grid, or grid is only meaningful when PBC is defined? On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > Dear users, > > If I dont define pbc=no, what is the default type for gromacs? Is it right > if I dont use pbc=no in my system while using grid for ns-type? > > 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.
Re: [gmx-users] PBC
Hi, See top of http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html regarding defaults. Or you can leave it blank and inspect what gmx grompp writes to the mdout.mdp. Whether any PBC setting makes sense depends what you're trying to do, which we don't know. Mark On Mon, Oct 5, 2015 at 9:37 AM mah maz wrote: > Dear users, > > If I dont define pbc=no, what is the default type for gromacs? Is it right > if I dont use pbc=no in my system while using grid for ns-type? > > 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC
Dear users, If I dont define pbc=no, what is the default type for gromacs? Is it right if I dont use pbc=no in my system while using grid for ns-type? 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.
Re: [gmx-users] PBC in a closed box.
Thanks for you answer, I didn't think about it, but actually a spherical droplet will be more ideal to this project than a cubic box. Thanks -R. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of André Farias de Moura Sent: Tuesday, August 4, 2015 1:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PBC in a closed box. choosing the electrostatic treatment seems to be the least of your problems: once you turn off the PBC, water molecules will coalesce into a spherical droplet in order to minimize the surface energy, so you first have to ask yourself if a nanometric water droplet suits your needs. Not a simulation issue, rather a surface chemistry fact. On Tue, Aug 4, 2015 at 2:24 PM, Rodney Versace Babilonia < rvers...@ccny.cuny.edu> wrote: > Hi all, > > I am trying to simulate the effusion process of water through hole in a > very thin film. The film is partitioning the water box, I wish to count the > numbers of waters before and after the simulation in each compartment, but > I am afraid that the use of periodic boundary conditions will make waters > from one side going to the other side through the boundaries and that > affect my counting, in case I turn off the PBC, what kind of electrostatic > treatment should I use? > > Thanks > > -Rod > > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC in a closed box.
choosing the electrostatic treatment seems to be the least of your problems: once you turn off the PBC, water molecules will coalesce into a spherical droplet in order to minimize the surface energy, so you first have to ask yourself if a nanometric water droplet suits your needs. Not a simulation issue, rather a surface chemistry fact. On Tue, Aug 4, 2015 at 2:24 PM, Rodney Versace Babilonia < rvers...@ccny.cuny.edu> wrote: > Hi all, > > I am trying to simulate the effusion process of water through hole in a > very thin film. The film is partitioning the water box, I wish to count the > numbers of waters before and after the simulation in each compartment, but > I am afraid that the use of periodic boundary conditions will make waters > from one side going to the other side through the boundaries and that > affect my counting, in case I turn off the PBC, what kind of electrostatic > treatment should I use? > > Thanks > > -Rod > > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC in a closed box.
Hi all, I am trying to simulate the effusion process of water through hole in a very thin film. The film is partitioning the water box, I wish to count the numbers of waters before and after the simulation in each compartment, but I am afraid that the use of periodic boundary conditions will make waters from one side going to the other side through the boundaries and that affect my counting, in case I turn off the PBC, what kind of electrostatic treatment should I use? Thanks -Rod -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC issue
If you just want to make a new, larger water box, try editconf to make the box larger and then genbox to add water. Any help beyond than that requires us to guess at at least four questions: What is an "unloading simulation" How did you "pull a protein" What exactly do you mean by "both ends of the protein run out of the boundary after pulling" Where should your protein ends connect? You'll likely get more help if you can be more specific about what you did and what the problem is. CHris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of tm651209 Sent: 03 July 2015 06:29 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] PBC issue Dear all, I pulled a protein using pdc=xyz, and want to do unloading simulation. The problem is both ends of the protein run out of the boundary after pulling. After unloading for a while, I found that both ends did not connect to where they should connect. Is there a way that I can regenerate the water box, so that the whole protein can stay inside. Therefore, I can use it as a initial state for unloading simulation. Thanks very much. Regards. -- 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] PBC issue
Dear all, I pulled a protein using pdc=xyz, and want to do unloading simulation. The problem is both ends of the protein run out of the boundary after pulling. After unloading for a while, I found that both ends did not connect to where they should connect. Is there a way that I can regenerate the water box, so that the whole protein can stay inside. Therefore, I can use it as a initial state for unloading simulation. Thanks very much. Regards. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC "no domain decomposition" error
Never mind my previous message. When I included periodicmolecule = yes in the mdp file, I believe that took care of the problem. Thanks, Jon - Hey! I ran into an issue when simulating graphene sheets with periodic boundary conditions. It said: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.685 nm I figured that was due to the apparent bond length of the carbons connected across the box, so I set -rdd to be 0.2 nm and now the simulation seems to be running fine. Is the -rdd command ignoring the bonds completely for the simulation, or still using bonds across the box edges once PBC is implemented? Thank you! Jon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC "no domain decomposition" error
It is my understanding that PBC will be (and really must be) taken into account whenever the bonds across the box are present in your topology and periodic-molecules is enabled in your mdp. Whether the particle population is now optimally decomposed to utilize the number of cores you've got is another question. Alex jace> Hey! jace> I ran into an issue when simulating graphene sheets with periodic boundary jace> conditions. It said: jace> There is no domain decomposition for 8 nodes that is compatible with the jace> given box and a minimum cell size of 4.685 nm jace> I figured that was due to the apparent bond length of the carbons jace> connected across the box, so I set -rdd to be 0.2 nm and now the jace> simulation seems to be running fine. jace> Is the -rdd command ignoring the bonds completely for the simulation, or jace> still using bonds across the box edges once PBC is implemented? jace> Thank you! jace> Jon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC "no domain decomposition" error
Hey! I ran into an issue when simulating graphene sheets with periodic boundary conditions. It said: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.685 nm I figured that was due to the apparent bond length of the carbons connected across the box, so I set -rdd to be 0.2 nm and now the simulation seems to be running fine. Is the -rdd command ignoring the bonds completely for the simulation, or still using bonds across the box edges once PBC is implemented? Thank you! Jon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pbc=z, applying pbc only along the z-direction
Hi Gromacs users, I have a confined system in both x and y directions. Gromacs offer 3 options for pbc=xyz or no or xy. Is there a way we can implement the pbc only along the z direction ? As I am using cutoff methods for electrostatistics one way to do this is to put some empty space (larger than the biggest interaction cutoff) and apply pbc in all 3 directions. But this would hamper the efficiency due to the way the domain decomposition is done. Any better alternatives ? Thanks. -- Cheers !!! Sridhar Kumar Kannam :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/15/14 3:12 PM, shahab shariati wrote: Dear Justin Thanks for your answer. You said " The raw output of g_traj in this case is not very useful " I want to know position and location of drug molecules relative to the DPPC bilayer during simulation time. In your opinion, how should I use this tool (g_traj)? I wouldn't. You can extract the needed information with a couple of steps of post-processing, but it's not worth it when g_dist will do this with no extra effort. Is g_dist appropriate for obtaining distance between center of mass of the drug molecules and DPPC lipid bilayer as a function of simulation time? Yes, use g_dist. But the x- and y- components aren't useful, so the (absolute value of) the z-component of the distance is what you need. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin Thanks for your answer. You said " The raw output of g_traj in this case is not very useful " I want to know position and location of drug molecules relative to the DPPC bilayer during simulation time. In your opinion, how should I use this tool (g_traj)? Is g_dist appropriate for obtaining distance between center of mass of the drug molecules and DPPC lipid bilayer as a function of simulation time? Best wishes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/15/14 12:11 PM, shahab shariati wrote: Dear Justin Very very thanks for your time and consideration. Excuse me for many questions. I want to make sure my trajectory is valid and accurate for analysis and then for writing related paper. It is. My last question is that can I use this trajectory for doing analysis such as g_traj, g_dist, g_density, g_rdf, g_order, g_msd, g_hbond .? Sure. Gromacs tools handle PBC effects just fine. You're getting hung up on something that's simply measured crudely. The absolute z-coordinate in this case means very little, precisely for the reasons we've been saying. The difference in z-coordinate between the drug molecules and the bilayer, provided that it is measured consistently, is a much more informative metric, assuming you're using it to indicate binding events. The raw output of g_traj in this case is not very useful. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin Very very thanks for your time and consideration. Excuse me for many questions. I want to make sure my trajectory is valid and accurate for analysis and then for writing related paper. My last question is that can I use this trajectory for doing analysis such as g_traj, g_dist, g_density, g_rdf, g_order, g_msd, g_hbond .? Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/15/14 4:52 AM, shahab shariati wrote: Dear Tsjerk Thanks for your reply. I think that there is another problem, except for visualization. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC lipid bilayer (black line) as a function of simulation time, using g_traj tool. The related figure is in following link: https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0 This Figure is not normal and usual. Sure it is. It may just not be the aesthetically pleasing output you want. What is your opinion about this issue? You're asking the same questions that were answered last week: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092153.html Yes, your plot is normal. Again, as I said in the linked message, there is no "side" in a periodic system. You have a continuous water layer. Your molecules simply diffuse around in it. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Tsjerk Thanks for your reply. I think that there is another problem, except for visualization. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC lipid bilayer (black line) as a function of simulation time, using g_traj tool. The related figure is in following link: https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0 This Figure is not normal and usual. What is your opinion about this issue? Best wishes, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
Hi, Just a small side note. There's nothing intrinsically nonsensical about translating more than a box size. The PBC are translation invariant, so you can do anything and have the system be fine. However, for visualization, translating one box length, and put the stuff back in the box, makes as much sense as doing nothing at all. Cheers, Tsjerk On Sep 14, 2014 3:55 PM, "Justin Lemkul" wrote: > > > On 9/14/14 9:52 AM, shahab shariati wrote: > >> Dear Justin >> >> >> I did following: >> >> >> trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9 >> >> Based on your reply*, *I translated all system along the z. >> >> I used x and y according to box dimension. >> >> I used 9, instead of z dimension (8.30034), for z. >> >> When I see **.xtc using vmd, problem was not solved. >> >> Should I increase or decrease z value for -trans option? >> >> > Start by following what I've told you: > > 1. Do not change x and y; set them to zero in -trans > 2. A value of 9 for z makes no sense if your box is not that large; try 8 > or less > 3. Use -pbc mol when translating > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/14/14 10:29 AM, shahab shariati wrote: Dear Justin Based on your previous reply, I used following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -pbc mol –trans 0 0 7 When I see **.xtc using vmd, unfortunately, problem was not solved. Please see the following link: https://www.dropbox.com/s/345o7lvc9z4jwln/figure%204.TIF?dl=0 From that picture, it is clear that it is simply impossible to gather all of the drug molecules on one side of the membrane. They have bound to both sides; there's no changing that since it's not an imaging issue. If some were bound and others were simultaneously still free in the water layer, it could be done. In this case, it cannot. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin Based on your previous reply, I used following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -pbc mol –trans 0 0 7 When I see **.xtc using vmd, unfortunately, problem was not solved. Please see the following link: https://www.dropbox.com/s/345o7lvc9z4jwln/figure%204.TIF?dl=0 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/14/14 9:52 AM, shahab shariati wrote: Dear Justin I did following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9 Based on your reply*, *I translated all system along the z. I used x and y according to box dimension. I used 9, instead of z dimension (8.30034), for z. When I see **.xtc using vmd, problem was not solved. Should I increase or decrease z value for -trans option? Start by following what I've told you: 1. Do not change x and y; set them to zero in -trans 2. A value of 9 for z makes no sense if your box is not that large; try 8 or less 3. Use -pbc mol when translating -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin I did following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9 Based on your reply*, *I translated all system along the z. I used x and y according to box dimension. I used 9, instead of z dimension (8.30034), for z. When I see **.xtc using vmd, problem was not solved. Should I increase or decrease z value for -trans option? Please see the following link: https://www.dropbox.com/s/ocahn2yzudwcj3z/figure%203.TIF?dl=0 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/14/14 8:58 AM, shahab shariati wrote: Dear Justin I did MD simulation on the NPT ensemble: pcoupl = Berendsen pcoupltype = semiisotropic ref_p = 1.0 In this condition, to solve this problem, what should I do? I have already said a few times what to do. Try running trjconv and see what you get rather than waiting for email responses. You'll accomplish more. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin I did MD simulation on the NPT ensemble: pcoupl = Berendsen pcoupltype = semiisotropic ref_p = 1.0 In this condition, to solve this problem, what should I do? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/14/14 8:43 AM, shahab shariati wrote: Dear Justin Thanks for your reply. I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug molecules) are seen in other side of bilayer (bottom). I really do not know what thing has to be translated. Should I shift all components of my system (DPPC, drug, and water molecules) along z or only drug molecules? Translate the whole system. The dimensions of my system in final gro file are as follows: 6.46063 6.57889 8.30034 Based on your reply (The exact magnitude depends on the dimensions of the system), should I use following command: trjconv –trans 6.46063 6.57889 8.30034 If you used pressure coupling, no, because the box dimensions will change over time. Moreover, you do not want to change x and y. As I said before, you want to translate along z. Try a few values and see if you get a reasonable result. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin Thanks for your reply. I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug molecules) are seen in other side of bilayer (bottom). I really do not know what thing has to be translated. Should I shift all components of my system (DPPC, drug, and water molecules) along z or only drug molecules? The dimensions of my system in final gro file are as follows: 6.46063 6.57889 8.30034 Based on your reply (The exact magnitude depends on the dimensions of the system), should I use following command: trjconv –trans 6.46063 6.57889 8.30034 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/13/14 7:59 AM, shahab shariati wrote: Dear Justin you said " The -trans option takes a vector where you specify the amount of translation to apply " I do not know what vector should be considered in -trans option. Well, what have you tried? You need to shift your system along z, the direction doesn't really matter. The exact magnitude depends on the dimensions of the system. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin you said " The -trans option takes a vector where you specify the amount of translation to apply " I do not know what vector should be considered in -trans option. please guide me to solve this problem as soon as possible. Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/11/14 1:51 PM, shahab shariati wrote: Dear Justin Very thanks for your answer. Unfortunately, I am beginner in MD simulation of bilayer membrane systems. Based on your answer (You can try the translation options of trjconv in conjunction with -pbc mol), should I use following command? trjconv –trans –pbc mol The -trans option takes a vector where you specify the amount of translation to apply. See trjconv -h. -Justin trjconv –pbc nojump Best wishes -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Justin Very thanks for your answer. Unfortunately, I am beginner in MD simulation of bilayer membrane systems. Based on your answer (You can try the translation options of trjconv in conjunction with -pbc mol), should I use following command? trjconv –trans –pbc mol trjconv –pbc nojump Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
On 9/11/14 8:01 AM, shahab shariati wrote: Dear gromacs users When I see trajectory file using vmd, there is state showed in following link: https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0 in initial structure, all 4 drugs were inserted in water phase, in one side of bilayer. Is this state normal? Yes, because there's no such thing as a "side" in a periodic system. You have a water layer that is continuous in z, so the molecules are free to diffuse around as they please. It may not be possible to re-image the trajectory such that all of the drug molecules are positioned in the same region in the unit cell. You can try the translation options of trjconv (in conjunction with -pbc mol) to try to shift the system up or down to get everything to fit, but then of course the lipids can jump around. Perhaps additional calls to trjconv can account for that (i.e. another round of -pbc nojump after translating). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear gromacs users When I see trajectory file using vmd, there is state showed in following link: https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0 in initial structure, all 4 drugs were inserted in water phase, in one side of bilayer. Is this state normal? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Gromacs users Unfortunately, no one did not answer my previous question about selection of appropriate option for trjconv -pbc to solve pbc problem. For preparation of initial system, I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC lipid bilayer (black line) as a function of simulation time, using g_traj tool. The related figure is in following link: https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0 Do this state is related to pbc problem? How to solve this issue? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
Also if you want to fix the position on the centre of mass (no rotating or translating) try -pbc nojump Followed by -fit rot+trans Remember to use you new .xtc from your no jump command for the -fit command. Then view in vmd and your molecules will not jump, rotate, or translate around the box. Mike On 09/09/2014 15:12, "Michael Carter" wrote: >Hi, > >Try -pbc nojump > >Best, >Mike > >On 09/09/2014 15:11, "shahab shariati" wrote: > >>Dear gromacs users >> >>I did MD simulation of my system containing DPPC lipids + water molecule >>and 4 drug molecules. >> >>I saw trajectory file using VMD. >> >>Unfortunately, drug molecules jump across the box. >> >>How to resolve this PBC problem? >> >>which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in >>trjconv tool is appropriate for my case? >> >> >>Any help will highly appreciated. >>-- >>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. > >The Institute of Cancer Research: Royal Cancer Hospital, a charitable >Company Limited by Guarantee, Registered in England under Company No. >534147 with its Registered Office at 123 Old Brompton Road, London SW7 >3RP. > >This e-mail message is confidential and for use by the addressee only. >If the message is received by anyone other than the addressee, please >return the message to the sender by replying to it and then delete the >message from your computer and network. >-- >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. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
Hi, Try -pbc nojump Best, Mike On 09/09/2014 15:11, "shahab shariati" wrote: >Dear gromacs users > >I did MD simulation of my system containing DPPC lipids + water molecule >and 4 drug molecules. > >I saw trajectory file using VMD. > >Unfortunately, drug molecules jump across the box. > >How to resolve this PBC problem? > >which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in >trjconv tool is appropriate for my case? > > >Any help will highly appreciated. >-- >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. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in trjconv tool is appropriate for my case? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC only on x and y in an NPT ensemble
Dear all I would like to simulate coarse grained thin polymer films supported on a wall or a substrate (I don't really mind) but with the one interface to be free. I would like to do this under NPT conditions. I would expect that this can only be done by putting pbc=xy, as in the to the following study: http://pubs.acs.org/doi/abs/10.1021/ma102567s but this option is not supported in GROMACS without the usage of walls. Is there any other way to simulated supported films in GROMACS under NPT conditions? Thanks in advance, Tommy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problems??
On 5/23/14, 2:51 PM, Steve Seibold wrote: My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus I have tried all combinations of "trjconv -pbc -center -box center" and nothing works..I was able to get online and find a tutorial that says trjconv -pbc mol, should stop the problem, but this failedIsn't there a way for the protein and water to be wrapped or COM calculations done DURING MD to remove translation, rotation so that post-MD modification of trajectories is unnecessary??...If I make an index group of the The integration doesn't need to follow our visualization convenience, so there's no reason to sacrifice performance to re-wrap coordinates on the fly. N-terminus of the protein this problems goes away or if I use the whole protein...It is only when I attempt to get the rms of the C-terminus region that I get this graphing problem (traj plots look like Histograms)Not sure what this means since if I observe the trajectories in VMD the whole protein breaks up Centering a single protein within a box should be very easy using any of the options you have posted. trjconv -pbc mol -ur compact -center should be all that's necessary for a simple system like this. Are you sure the box is large enough to accommodate the protein? If it keeps "breaking" in spite of trjconv, that might suggest your box is not suitable, such that re-imaging can't fix things. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problems??
My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus I have tried all combinations of "trjconv -pbc -center -box center" and nothing works..I was able to get online and find a tutorial that says trjconv -pbc mol, should stop the problem, but this failedIsn't there a way for the protein and water to be wrapped or COM calculations done DURING MD to remove translation, rotation so that post-MD modification of trajectories is unnecessary??...If I make an index group of the N-terminus of the protein this problems goes away or if I use the whole protein...It is only when I attempt to get the rms of the C-terminus region that I get this graphing problem (traj plots look like Histograms)Not sure what this means since if I observe the trajectories in VMD the whole protein breaks up Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
Dear Justin, you’re right. The problem was the system was not center properly in the initial .gro file. Now it works. Thank you very much. Juan C. On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote: > Dear Mark, > > I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. > There are two possibilities: 1. You built the system wrong and trjconv can't fix it. Without the full sequence of commands used to build the system, no one can provide any advice here. Providing an image that shows the unit cell ("pbc box" in the Tcl window in VMD) can also be informative in this regard. 2. This is a PBC issue that should be resolvable, probably within a few iterations of trjconv. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow. Often times, it helps to start with a new .tpr file that has the system centered properly when remove jumps, etc. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote: Dear Mark, I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. There are two possibilities: 1. You built the system wrong and trjconv can't fix it. Without the full sequence of commands used to build the system, no one can provide any advice here. Providing an image that shows the unit cell ("pbc box" in the Tcl window in VMD) can also be informative in this regard. 2. This is a PBC issue that should be resolvable, probably within a few iterations of trjconv. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow. Often times, it helps to start with a new .tpr file that has the system centered properly when remove jumps, etc. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
Dear Mark, I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. Juan C. > > Dear Justin, > > thank you. I’ve tried the following but neither of them worked, I get the same result. > > trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact > > trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc mol -ur compact You need to use numbers. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
On May 16, 2014 7:03 PM, "Juan Munoz-Garcia" < juan.munoz-gar...@bioch.ox.ac.uk> wrote: > > Dear Justin, > > thank you. I’ve tried the following but neither of them worked, I get the same result. > > trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact > > trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc mol -ur compact You need to use numbers. Mark > > This is the last line of my input.gro file > > 19.51671 19.51671 13.80040 0.0 0.0 0.0 0.0 9.75836 9.75836 > > Juan C. > > > Your system was probably centered at z=0 instead of z = z_box/2 (commands used > for building the system would also help - I guess I should have been more > clear), hence it's getting split across PBC. trjconv -trans in conjunction with > -pbc mol should be what you need. > > -Justin > > -- > > Begin forwarded message: > > From: Juan Carlos Munoz Garcia > > Subject: Re: PBC correction to visualize a protein-membrane structure > Date: 16 May 2014 14:08:50 BST > To: > > > Thank you Justin, > > please find a dropbox link to the image below. > > I’ve used > > trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole > trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center > > and different combinations of those > > https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png > > Thank you. > Regards. > Juan C. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
Dear Justin, thank you. I’ve tried the following but neither of them worked, I get the same result. trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc mol -ur compact This is the last line of my input.gro file 19.51671 19.51671 13.80040 0.0 0.0 0.0 0.0 9.75836 9.75836 Juan C. Your system was probably centered at z=0 instead of z = z_box/2 (commands used for building the system would also help - I guess I should have been more clear), hence it's getting split across PBC. trjconv -trans in conjunction with -pbc mol should be what you need. -Justin -- Begin forwarded message: From: Juan Carlos Munoz Garcia mailto:juan.munoz-gar...@bioch.ox.ac.uk>> Subject: Re: PBC correction to visualize a protein-membrane structure Date: 16 May 2014 14:08:50 BST To: mailto:gromacs.org_gmx-users@maillist.sys.kth.se>> Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png Thank you. Regards. Juan C. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
On 5/16/14, 9:08 AM, Juan Munoz-Garcia wrote: Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png Your system was probably centered at z=0 instead of z = z_box/2 (commands used for building the system would also help - I guess I should have been more clear), hence it's getting split across PBC. trjconv -trans in conjunction with -pbc mol should be what you need. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png Thank you. Regards. Juan C. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC correction to visualize a protein-membrane structure
On 5/16/14, 4:04 AM, Juan Munoz-Garcia wrote: Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I still get the same structure. Even more weird is that when I turn on the periodic images option in vmd I still don’t see the right protein embedded into the lipid bilayer. As this can’t be a real effect of minimisation, I'd like to ask for your advice. The mailing list does not accept attachments. Please post links to images or files to download. An exact sequence of commands would be useful, as well. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC correction to visualize a protein-membrane structure
Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I still get the same structure. Even more weird is that when I turn on the periodic images option in vmd I still don’t see the right protein embedded into the lipid bilayer. As this can’t be a real effect of minimisation, I'd like to ask you for advice. Thank you. Juan C. Munoz-Garcia [cid:37CD9EEE-6F74-43E1-A009-4D0D487104FD] -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.