[gmx-users] Triclinic box is too skewed
Hi all,
I apply a deform at the xy direction of the box, the rate is 0.01 nm/ps but
I met this error :
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 1.06717e+01, 0.0e+00, 0.0e+00}
Box[1]={ 5.34312e+00, 1.06717e+01, 0.0e+00}
Box[2]={ 0.0e+00, 0.0e+00, 1.06717e+01}
Can not fix pbc.
Any suggestions about this? Thanks
Regards
--
*Jun ZHOU*
Postgraduate Student ,
Room 117, Building 36
Department of Civil Engineering,
Monash University,
Victoria 3800, Australia.
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[gmx-users] about correct methodology to run MD of small molecule in gromacs
Dear Gromacs users, As I have referred before I am simulating small molecules (nucleosides) (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the end I want to select the most stable structure from the trajectory for the next steps. What would be the best methodology to use to run a molecular dynamics for this?: 1) Run an anneling and collect the different frames for the trajectory and then at the end analyze the RSMD, free energy and maybe do clustering for the different frames to select the most stable structure? 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella sampling"?, the only problem here is that I want all dihedral angles to rotate and I do not know how to do this. 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in which I generate the free energy from different lambda values from consecutive simulations. Any suggestions? I am not sure how to proceed correctly here. Kindly, Lazaro -- 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] Question about Mean Square Displacement (MSD)
What are you trying to calculate MSD for? I doubt that would be sufficient sampling to calculate the diffusion coefficient of anything except maybe water. For lipids, you don't start getting accurate readings until you reach a **lag** time of 10 ns, and you need 100s of ns of data to get a good reading even at that lag time. That's with many lipids in a bilayer. I don't have experience with calculating diffusion coefficients for proteins, but I'd imagine you need microseconds of sampling, since they're much slower tumblers and you usually only have one per simulation box. Your save rate is fine, and could be even more granular. On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani wrote: > *Message sent from a system outside of UConn.* > > > Thanks, Kevin, > I am looking for the MSD vs lag plot. I use the saved frames that specified > in mdp file. Is that the problem? I saved positions every 10 ps for a 6000 > ps simulation. should I lower this or is there another way for using more > trajectories? > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > > > Hi, > > > > Are you talking about the reported diffusion coefficient or the MSD vs > lag > > plot? You should be very careful about where you fit. By default, Gromacs > > calculates MSDs at much longer lag times than you typically have good > data > > for. Use the -beginfit and -endfit options to restrict the fit to the lag > > times where the MSD plot is linear. > > > > >I use trjconv command and use the output .gro file > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > > wrote: > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > Unless you give you give details how you calculate the MSD it will not > be > > > possible to help. > > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > > > Arun > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > > wrote: > > > > > > > Hi, > > > > I am trying to post-processing my results and calculate MSD (mean > > square > > > > displacement) but my answer is different from the MSD value that > > GROMACS > > > > calculated. I use trjconv command and use the output .gro file. I > tried > > > to > > > > understand the GROMACS code but I am not a good programmer. Is there > > any > > > > specific detail except the Einstein relation in the manual? > > > > > > > > sorry if here is not the right place to ask this question. > > > > Best regards. > > > > > > > > Sina Omrani. > > > > -- > > > > 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] Question about Mean Square Displacement (MSD)
Thanks, Kevin, I am looking for the MSD vs lag plot. I use the saved frames that specified in mdp file. Is that the problem? I saved positions every 10 ps for a 6000 ps simulation. should I lower this or is there another way for using more trajectories? On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > Hi, > > Are you talking about the reported diffusion coefficient or the MSD vs lag > plot? You should be very careful about where you fit. By default, Gromacs > calculates MSDs at much longer lag times than you typically have good data > for. Use the -beginfit and -endfit options to restrict the fit to the lag > times where the MSD plot is linear. > > >I use trjconv command and use the output .gro file > > This doesn't make much sense, how many frames are you analyzing? > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > wrote: > > > *Message sent from a system outside of UConn.* > > > > > > Unless you give you give details how you calculate the MSD it will not be > > possible to help. > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > Arun > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > wrote: > > > > > Hi, > > > I am trying to post-processing my results and calculate MSD (mean > square > > > displacement) but my answer is different from the MSD value that > GROMACS > > > calculated. I use trjconv command and use the output .gro file. I tried > > to > > > understand the GROMACS code but I am not a good programmer. Is there > any > > > specific detail except the Einstein relation in the manual? > > > > > > sorry if here is not the right place to ask this question. > > > Best regards. > > > > > > Sina Omrani. > > > -- > > > 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] Question about Mean Square Displacement (MSD)
Hi, Are you talking about the reported diffusion coefficient or the MSD vs lag plot? You should be very careful about where you fit. By default, Gromacs calculates MSDs at much longer lag times than you typically have good data for. Use the -beginfit and -endfit options to restrict the fit to the lag times where the MSD plot is linear. >I use trjconv command and use the output .gro file This doesn't make much sense, how many frames are you analyzing? On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth wrote: > *Message sent from a system outside of UConn.* > > > Unless you give you give details how you calculate the MSD it will not be > possible to help. > Are you using unwrapped co-ordinates in your calculations for MSD? > > Arun > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > wrote: > > > Hi, > > I am trying to post-processing my results and calculate MSD (mean square > > displacement) but my answer is different from the MSD value that GROMACS > > calculated. I use trjconv command and use the output .gro file. I tried > to > > understand the GROMACS code but I am not a good programmer. Is there any > > specific detail except the Einstein relation in the manual? > > > > sorry if here is not the right place to ask this question. > > Best regards. > > > > Sina Omrani. > > -- > > 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] Question about Mean Square Displacement (MSD)
Unless you give you give details how you calculate the MSD it will not be possible to help. Are you using unwrapped co-ordinates in your calculations for MSD? Arun On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani wrote: > Hi, > I am trying to post-processing my results and calculate MSD (mean square > displacement) but my answer is different from the MSD value that GROMACS > calculated. I use trjconv command and use the output .gro file. I tried to > understand the GROMACS code but I am not a good programmer. Is there any > specific detail except the Einstein relation in the manual? > > sorry if here is not the right place to ask this question. > Best regards. > > Sina Omrani. > -- > 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] Question about Mean Square Displacement (MSD)
Hi, I am trying to post-processing my results and calculate MSD (mean square displacement) but my answer is different from the MSD value that GROMACS calculated. I use trjconv command and use the output .gro file. I tried to understand the GROMACS code but I am not a good programmer. Is there any specific detail except the Einstein relation in the manual? sorry if here is not the right place to ask this question. Best regards. Sina Omrani. -- 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] Artifact in pull-pbc-ref-prev-step-com
Dear all, To generate the initial configurations for umbrella sampling, I conducted a simple pulling simulation by which a single-small molecule (mol_A) is being dragged along -Z from water into the body of a thin film. Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and "pull-group1-pbcatom = -1"* which cause a net shifting of the system along the pulling direction as soon as the mol_A reach to the thin film, please find below the pulling flags movie and plot in below links. Centering the thin film and mol_A could solve the issue, (echo 1 0 | trjconv -center yes) to some extent but still COM changes in the early stage below 2ns. , COM: https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 Movie in which the water molecules are hidden: https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv - gmx version 2020.1 - pull = yes pull-print-com = no pull-print-ref-value = yes pull-print-components= Yes pull-nstxout = 1000 pull-nstfout = 1000 pull-pbc-ref-prev-step-com = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Thin-film pull-group1-pbcatom = -1 pull-group2-name = mol_A pull-group2-pbcatom = 0 pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 1 2 pull-coord1-dim = N N Y pull-coord1-origin = 0.0 0.0 0.0 pull-coord1-vec = 0.0 0.0 -1.0 pull-coord1-start= yes pull-coord1-init = 0 pull-coord1-rate = 0.0005 pull-coord1-k= 5000 - I wonder if I could extract correct initial configuration from this trajectory? With correct initial configuration, I mean a set of gro file in which change from one from to another is the distance between the COM of the thin-film and mol_A? Thank you 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] Installation on iPad
Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of course, considering the new iPad OS released. Kind regards, Ali -- 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] Failed to find GROMACS magic number in trr frame header
Hi, No, some kind of breakage, e.g. a filesystem disappeared, or a file transfer was incomplete or the file was edited with some inappropriate tool. Mark On Sat, 18 Apr 2020 at 11:46, Mijiddorj B wrote: > Dear Justin, > > Thank you very much for your reply. I see. However, I have one more > question. Is it caused by usage of -noappend or other reasons? > > Best regards, > > Mijiddorj > > - > > > > Message: 1 > > Date: Fri, 17 Apr 2020 11:51:25 -0400 > > From: Justin Lemkul > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr > > frame header > > Message-ID: <77b40330-739a-c03e-85f2-1bc74b97c...@vt.edu> > > Content-Type: text/plain; charset=utf-8; format=flowed > > > > > > > > On 4/17/20 10:13 AM, Mijiddorj B wrote: > > > Dear GMX users, > > > > > > Hello, I performed MD simulation using gromacs 2018.7v. During this > > > simulation, the calculation was stopped because of the electric cut. > > Then, > > > I continued the simulation using "gmx mdrun with -noappend" in order to > > get > > > separate trajectory for the safety of data. After that, I would like to > > > concatenate the trr files. > > > However, I received following error message. > > > > > > How, can I concatenate these trajectories. > > > ** > > > Program: gmx trjcat, version 2018.7 > > > Source file: src/gromacs/fileio/trrio.cpp (line 114) > > > > > > Fatal error: > > > Failed to find GROMACS magic number in trr frame header, so this is > not a > > > trr > > > file! > > > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > > > > > Your file is corrupted and you will have to run that portion of the > > simulation again. > > > > -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. > -- 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] Failed to find GROMACS magic number in trr frame header
Dear Justin, Thank you very much for your reply. I see. However, I have one more question. Is it caused by usage of -noappend or other reasons? Best regards, Mijiddorj - > > Message: 1 > Date: Fri, 17 Apr 2020 11:51:25 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr > frame header > Message-ID: <77b40330-739a-c03e-85f2-1bc74b97c...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 4/17/20 10:13 AM, Mijiddorj B wrote: > > Dear GMX users, > > > > Hello, I performed MD simulation using gromacs 2018.7v. During this > > simulation, the calculation was stopped because of the electric cut. > Then, > > I continued the simulation using "gmx mdrun with -noappend" in order to > get > > separate trajectory for the safety of data. After that, I would like to > > concatenate the trr files. > > However, I received following error message. > > > > How, can I concatenate these trajectories. > > ** > > Program: gmx trjcat, version 2018.7 > > Source file: src/gromacs/fileio/trrio.cpp (line 114) > > > > Fatal error: > > Failed to find GROMACS magic number in trr frame header, so this is not a > > trr > > file! > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > Your file is corrupted and you will have to run that portion of the > simulation again. > > -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.
[gmx-users] Regarding use of harmonic wall model
Hello everyone, I want to create a gap between the first and last strand of a beta barrel so that I can put a new strand in between. So, I have generated an input file using charmm-gui and using its gromacs production file (production.mdp) to run the simulation. I want to use a harmonic wall model to disrupt the bonding between the first and last strand of the beta barrel but not getting how to do it . I have asked it before as well but I did not get any suggestion. Please kindly help me with this query if anybody has any idea regarding this. Thank you, -- Shashank Ranjan Srivastava Molecular Biophysics Laboratory Department of Biological Sciences, IISER-Bhopal, Madhya Pradesh -- 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.
