Re: [gmx-users] defining parameters in a separate itp file
Hi Justin, Thanks for your reply but am getting error suggesting a intermolecular chemical bond is not allowed: Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649) Fatal error: The intermolecular_interaction can not contain chemically bonding interactions [ molecules ] ; namenumber molA 1 molB 1 W 2420 [intermolecular_interactions] [ bonds ] 1 158 1 0.4 2000 This is coarse-grained model and as a simple test I used global atom numbers between two water single particles (intermolecular) but I get the same error. regards, Dave On Mon, Oct 28, 2019 at 5:58 AM Justin Lemkul wrote: > > > On 10/27/19 9:24 PM, Dave M wrote: > > Hi All, > > > > I am trying to define a bond between two molecules. Their parameters are > > defined in separate itp files: molA.itp and molB.itp. I know I can > > combine both the itp files but I am just wondering if I can define extra > > bonds/angles joining two molecules in a separate itp file taking care of > > atom numbers. To test it I defined an extra bond joining two atoms > (elastic > > bond) from two molecules in a separate bond.itp file but it does not look > > like molecules come close at all. > > Not sure this is a correct way. And, also is there a way I can print the > > bond parameters from tpr file to confirm whether all the bonds and angles > > are read from itp files. > > > > My top file looks like this > > > > #include "mol1.itp" > > > > #include "mol2.itp" > > > > #include "bond.itp" > > > > > > [ system ] > > > > test > > > > > > [ molecules ] > > > > ; namenumber > > > > molA 1 > > > > molB 1 > > You don't even need a separate .itp file. After you define [molecules], > you can add an [intermolecular_interactions] directive like so: > > [intermolecular_interactions] > [bonds] > atom_i atom_j b0 kb > > Note that atom_i and atom_j, unlike individual [moleculetype] > definitions, refer to the global atom numbers in the coordinate file. > > -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] Fatal Error when launching gromacs 2019.2 on GPU.
Hi, Indeed, the standard way provided by CUDA to expose a subset of GPUs to an application is the CUDA_VISIBLE_DEVICES (note the "S" ending); I did not realize that is something you were interested in, I thought you wanted to avoid using GPUs. Also note (for anyone interested), a when using a queue system, if node sharing is allowed, the scheduler should be set up to a correct CUDA_VISIBLE_DEVICES variable as well. Cheers, -- Szilárd On Mon, Oct 28, 2019 at 1:43 PM Artem Shekhovtsov wrote: > Hi, > > Thanks, setting this variable allowed me to start GROMACS without errors > using the CPU. > The problem is that this method prevents me from using other free GPUs on > the host, but I would like to do this. > I also found out that setting the CUDA_VISIBLE_DEVICE variable to available > GPUs at the time of launch allows us to solve this problem. > > Artem > > > On Sat, Oct 26, 2019 at 1:50 AM Szilárd Páll > wrote: > > > Hi, > > > > This is an issue in one of pre-detection checks that trips due to > > encountering exclusive / prohibited mode devices. > > > > You can work around this by entirely disabling the detection using the > > GMX_DISABLE_GPU_DETECTION environment variable. > > > > Cheers, > > -- > > Szilárd > > > > > > On Thu, Oct 17, 2019 at 5:01 PM Artem Shekhovtsov < > > job.shekhovt...@gmail.com> > > wrote: > > > > > Hello! > > > Problem: The launch of mdrun that does not require video cards exit > with > > > fatal error if at least one video card is busy on the host at that > time. > > > gmx mdrun -deffnm test -ntmpi 1 -ntomp 1 -nb cpu -bonded cpu > > > --- > > > Program: gmx mdrun, version 2019.2 > > > Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) > > > > > > Fatal error: > > > cudaFuncGetAttributes failed: all CUDA-capable devices are busy or > > > unavailable > > > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > --- > > > > > > I have this error in gromacs version 2019.2, 2019.3, 2020.beta. > > > Version - 2018.6 is not affected. > > > All version builds with the same flags. > > > > > > Archive with log files and gromacs build files > > > > > > > > > https://drive.google.com/file/d/1ahn7S69CU5yvAPlLWHryXmMzcGfdWVxP/view?usp=sharing > > > > > > > > > I would appreciate any help. > > > > > > Thanks, > > > Artem Shekhovtsov. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)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] Creating distance restraints between two atoms of different molecules
On 10/28/19 12:43 PM, Mustafa Tekpinar wrote: Hello everybody, I am trying to put a distance restraint between two atoms of different molecules, such as DNA and RNA . I created an index file that contains only these two atoms. Then, I called gmx genrestr with this index file. Now, I have an itp file, which includes a distance restraint. However, I have two questions here: 1. In positional restraints, the atoms numbers refers to the numbers in moleculetype section, not to the general gro file ordering. However, in my itp file, the numbers refers to the gro file numbering for both of the atoms. Is this correct? 2. Where should I call this itp file in my topology file? You should use the pull code to employ the restraint. While you can define [distance_restraints] under an [intermolecular_interactions] directive at the end of the system .top file, it will limit you in terms of domain decomposition and your run will be very slow. Use the pull code to apply a biasing potential, instead. -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] Creating distance restraints between two atoms of different molecules
Hello everybody, I am trying to put a distance restraint between two atoms of different molecules, such as DNA and RNA . I created an index file that contains only these two atoms. Then, I called gmx genrestr with this index file. Now, I have an itp file, which includes a distance restraint. However, I have two questions here: 1. In positional restraints, the atoms numbers refers to the numbers in moleculetype section, not to the general gro file ordering. However, in my itp file, the numbers refers to the gro file numbering for both of the atoms. Is this correct? 2. Where should I call this itp file in my topology file? Thanks in advance for your help, Mustafa -- Mustafa Tekpinar, PhD Pasteur Institute 25-28 Rue du Dr Roux 75015 Paris, France -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Fwd: gmx trjcat
Hi Paul, I though you mean converting the .gro files to .xtc file using *trjcat *(which was my initial question), sorry about that. I see now, I just used *trjconv* to convert gro file them to .xtc files and then ... . .gro trjconv> .xtc --trjcat> .xtc(or trr) Thanks Alex On Mon, Oct 28, 2019 at 11:18 AM Paul bauer wrote: > Hello, > > I think I understood your problem (or at least hope so). > The issue is that it is no longer possible to directly concatenate text > based trajectory files, so I showed a possible way to work around the > problem. > You can also go back to a previous version of GROMACS to perform the > concatenation, but I can't promise you that it will work. > > Please let me know if you need extra help to get this to work. > > @Justin, here is the change that added the check for binary file > formats: c232242c29fb3ca63c8e1027eb70477069decdd9 > > Cheers > > Paul > > On 28/10/2019 15:42, Alex wrote: > > Hi, > > Paul, > > I guess you understood the question wrongly. I have some *.gro files and > I > > want to concatenate them to have a trr (or xtc) trajectory. > > > > Justin, > > Yes indeed, It would be great if gmx trjcat could concatenate the gro > files. > > > > Regards, > > Alex > > > > On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul wrote: > > > >> > >> On 10/28/19 6:26 AM, Paul bauer wrote: > >>> Hello, > >>> > >>> this looks like a case of misleading documentation. Can you file an > >>> issue for this please on redmine.gromacs.org? > >>> So that we don't forgot to fix this for the next patch release? > >>> A possible work around for you can be that you first convert your > >>> files to e.g. XTC format, use trjcat to combine them and convert them > >>> back to GRO. > >>> > >> Out of curiosity, why was this file format removed as an input for > >> trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB > >> files to make a psuedo-trajectory for ensemble analysis was rather > >> handy. Converting to an intermediate binary format is a workaround, but > >> why add the extra step? Did the trjcat code need de-complicating? > >> > >> -Justin > >> > >>> Cheers > >>> > >>> Paul > >>> > >>> > >>> On 27/10/2019 19:47, Alex wrote: > Any comment on this, please? > Thanks > -- Forwarded message - > From: Alex > Date: Sat, Oct 26, 2019 at 9:38 AM > Subject: gmx trjcat > To: > > > Dear all, > I want to concatenate some gro file to have a trr or xtc trajectory > file > out of them as gro files are also acceptable as input files, > according the > gmx trjcat man page; > > Options to specify input files: > -f [<.xtc/.trr/...> [...]] (traj.xtc) > Trajectory: xtc trr cpt *gro* g96 pdb tng > > So, I fed the .gro files in as input files likes; > gmx trjcat -f c*.gro -o trajout.trr > > However, I get below error that; > Fatal error: > gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) > > Any comment is highly appreciated. > Regards, > Alex > >>> > >> -- > >> == > >> > >> 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. > > > -- > Paul Bauer, PhD > GROMACS Release Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] Fwd: gmx trjcat
Hello, I think I understood your problem (or at least hope so). The issue is that it is no longer possible to directly concatenate text based trajectory files, so I showed a possible way to work around the problem. You can also go back to a previous version of GROMACS to perform the concatenation, but I can't promise you that it will work. Please let me know if you need extra help to get this to work. @Justin, here is the change that added the check for binary file formats: c232242c29fb3ca63c8e1027eb70477069decdd9 Cheers Paul On 28/10/2019 15:42, Alex wrote: Hi, Paul, I guess you understood the question wrongly. I have some *.gro files and I want to concatenate them to have a trr (or xtc) trajectory. Justin, Yes indeed, It would be great if gmx trjcat could concatenate the gro files. Regards, Alex On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul wrote: On 10/28/19 6:26 AM, Paul bauer wrote: Hello, this looks like a case of misleading documentation. Can you file an issue for this please on redmine.gromacs.org? So that we don't forgot to fix this for the next patch release? A possible work around for you can be that you first convert your files to e.g. XTC format, use trjcat to combine them and convert them back to GRO. Out of curiosity, why was this file format removed as an input for trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB files to make a psuedo-trajectory for ensemble analysis was rather handy. Converting to an intermediate binary format is a workaround, but why add the extra step? Did the trjcat code need de-complicating? -Justin Cheers Paul On 27/10/2019 19:47, Alex wrote: Any comment on this, please? Thanks -- Forwarded message - From: Alex Date: Sat, Oct 26, 2019 at 9:38 AM Subject: gmx trjcat To: Dear all, I want to concatenate some gro file to have a trr or xtc trajectory file out of them as gro files are also acceptable as input files, according the gmx trjcat man page; Options to specify input files: -f [<.xtc/.trr/...> [...]] (traj.xtc) Trajectory: xtc trr cpt *gro* g96 pdb tng So, I fed the .gro files in as input files likes; gmx trjcat -f c*.gro -o trajout.trr However, I get below error that; Fatal error: gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) Any comment is highly appreciated. Regards, Alex -- == 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. -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Help with a failing test - gromacs 2019.4 - Test 42
Hi Szilard, I just found time to rerun the tests and your suggestion worked. Many thanks for this. Regards, T. On Wed, 16 Oct 2019 at 13:43, Szilárd Páll wrote: > Hi, > > The issue is an internal error triggered by the domain decomposition not > liking 14 cores in your CPU which lead to a prime rank count. > To ensure the tests pass I suggest trying to force only one device to be > used in make check, e.g. CUDA_VISIBLE_DEVICES=0 make check; alternatively > you can run the regressiontests manually. > > Cheers, > -- > Szilárd > > > On Thu, Oct 10, 2019 at 6:01 PM Raymond Arter > wrote: > > > Hi, > > > > When performing a "make check" on Gromacs 2019.4, I'm getting test 42 > > failing. > > It gives the error: > > > > Mdrun cannot use the requested (or automatic) number of ranks, > > retrying with 8 > > > > And the mdrun.out and md.log of swap_x reports: > > > > The number of ranks you selected (14) contains a large prime > factor > > 7. > > > > I've included the necessary parts of the logs below. Any help would be > > appreciated > > since I haven't come across this error before. > > > > Regards, > > > > T. > > > > > > CentOS Linux release 7.6.1810 (Core) > > CPU: Intel Xeon Gold 6132 > > Tesla V100 > > Cuda: 10.1 > > Driver: 418.40.04 > > > > Output of "make check" > > > > 42/46 Test #42: regressiontests/complex .***Failed 145.88 > sec > > > > GROMACS: gmx mdrun, version 2019.4 > > Executable: /gromacs/2019.4/gromacs-2019.4/build/bin/gmx > > Data prefix: /gromacs/2019.4/gromacs-2019.4 (source tree) > > Working dir: > > /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4 > > Command line: > > gmx mdrun -h > > > > Thanx for Using GROMACS - Have a Nice Day > > > > Mdrun cannot use the requested (or automatic) number of ranks, retrying > > with 8. > > > > Abnormal return value for ' gmx mdrun-nb cpu -notunepme >mdrun.out > > 2>&1' was 1 > > Retrying mdrun with better settings... > > Re-running orientation-restraints using CPU-based PME > > Re-running pull_geometry_angle using CPU-based PME > > Re-running pull_geometry_angle-axis using CPU-based PME > > Re-running pull_geometry_dihedral using CPU-based PME > > > > Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' > was > > -1 > > FAILED. Check mdrun.out, md.log file(s) in swap_x for swap_x > > > > Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' > was > > -1 > > FAILED. Check mdrun.out, md.log file(s) in swap_y for swap_y > > > > Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' > was > > -1 > > FAILED. Check mdrun.out, md.log file(s) in swap_z for swap_z > > 3 out of 55 complex tests FAILED > > > > From the following directory: > > > > > /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4/complex/swap_x > > and I get the same errors for swap_y and swap_z > > > > == mdrun.out == > > > > GROMACS: gmx mdrun, version 2019.4 > > Executable: /gromacs/2019.4/gromacs-2019.4/build/bin/gmx > > Data prefix: /gromacs/2019.4/gromacs-2019.4 (source tree) > > Working dir: > > > > > /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4/complex/swap_x > > Command line: > > gmx mdrun -notunepme > > > > Reading file topol.tpr, VERSION 2019.4 (single precision) > > Changing nstlist from 10 to 50, rlist from 1.011 to 1.137 > > > > --- > > Program: gmx mdrun, version 2019.4 > > Source file: src/gromacs/domdec/domdec_setup.cpp (line 764) > > MPI rank:0 (out of 14) > > > > Fatal error: > > The number of ranks you selected (14) contains a large prime factor 7. In > > most > > cases this will lead to bad performance. Choose a number with smaller > prime > > factors or set the decomposition (option -dd) manually. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > > == md.out == > > > > Changing nstlist from 10 to 50, rlist from 1.011 to 1.137 > > > > Initializing Domain Decomposition on 14 ranks > > Dynamic load balancing: locked > > Minimum cell size due to atom displacement: 0.692 nm > > Initial maximum distances in bonded interactions: > > two-body bonded interactions: 0.403 nm, Exclusion, atoms 184 187 > > multi-body bonded interactions: 0.403 nm, Ryckaert-Bell., atoms 184 187 > > Minimum cell size due to bonded interactions: 0.443 nm > > Maximum distance for 3 constraints, at 120 deg. angles, all-trans: 0.459 > nm > > Estimated maximum distance required for P-LINCS: 0.459 nm > > > > --- > > Program: gmx mdrun, version 2019.4 > > Source file: src/gromacs/domdec/domdec_setup.cpp (line 764) > > MPI rank:0 (out of 14) > > > > Fatal error: > > The number of ranks you selected (14) contains a large prime factor 7. In > > most > > cases this
Re: [gmx-users] Fwd: gmx trjcat
On 10/28/19 10:42 AM, Alex wrote: Hi, Paul, I guess you understood the question wrongly. I have some *.gro files and I want to concatenate them to have a trr (or xtc) trajectory. I don't think Paul misunderstood at all. The version of trjcat that you're using does not support an operation it once did - to concatenate coordinate files. You have to do an extra step, converting each .gro to an .xtc frame, before invoking trjcat. His solution gets around your problem. -Justin Justin, Yes indeed, It would be great if gmx trjcat could concatenate the gro files. Regards, Alex On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul wrote: On 10/28/19 6:26 AM, Paul bauer wrote: Hello, this looks like a case of misleading documentation. Can you file an issue for this please on redmine.gromacs.org? So that we don't forgot to fix this for the next patch release? A possible work around for you can be that you first convert your files to e.g. XTC format, use trjcat to combine them and convert them back to GRO. Out of curiosity, why was this file format removed as an input for trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB files to make a psuedo-trajectory for ensemble analysis was rather handy. Converting to an intermediate binary format is a workaround, but why add the extra step? Did the trjcat code need de-complicating? -Justin Cheers Paul On 27/10/2019 19:47, Alex wrote: Any comment on this, please? Thanks -- Forwarded message - From: Alex Date: Sat, Oct 26, 2019 at 9:38 AM Subject: gmx trjcat To: Dear all, I want to concatenate some gro file to have a trr or xtc trajectory file out of them as gro files are also acceptable as input files, according the gmx trjcat man page; Options to specify input files: -f [<.xtc/.trr/...> [...]] (traj.xtc) Trajectory: xtc trr cpt *gro* g96 pdb tng So, I fed the .gro files in as input files likes; gmx trjcat -f c*.gro -o trajout.trr However, I get below error that; Fatal error: gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) Any comment is highly appreciated. Regards, Alex -- == 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. -- == 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] Fwd: gmx trjcat
Hi, Paul, I guess you understood the question wrongly. I have some *.gro files and I want to concatenate them to have a trr (or xtc) trajectory. Justin, Yes indeed, It would be great if gmx trjcat could concatenate the gro files. Regards, Alex On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul wrote: > > > On 10/28/19 6:26 AM, Paul bauer wrote: > > Hello, > > > > this looks like a case of misleading documentation. Can you file an > > issue for this please on redmine.gromacs.org? > > So that we don't forgot to fix this for the next patch release? > > A possible work around for you can be that you first convert your > > files to e.g. XTC format, use trjcat to combine them and convert them > > back to GRO. > > > > Out of curiosity, why was this file format removed as an input for > trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB > files to make a psuedo-trajectory for ensemble analysis was rather > handy. Converting to an intermediate binary format is a workaround, but > why add the extra step? Did the trjcat code need de-complicating? > > -Justin > > > Cheers > > > > Paul > > > > > > On 27/10/2019 19:47, Alex wrote: > >> Any comment on this, please? > >> Thanks > >> -- Forwarded message - > >> From: Alex > >> Date: Sat, Oct 26, 2019 at 9:38 AM > >> Subject: gmx trjcat > >> To: > >> > >> > >> Dear all, > >> I want to concatenate some gro file to have a trr or xtc trajectory file > >> out of them as gro files are also acceptable as input files, > >> according the > >> gmx trjcat man page; > >> > >> Options to specify input files: > >> -f [<.xtc/.trr/...> [...]] (traj.xtc) > >> Trajectory: xtc trr cpt *gro* g96 pdb tng > >> > >> So, I fed the .gro files in as input files likes; > >> gmx trjcat -f c*.gro -o trajout.trr > >> > >> However, I get below error that; > >> Fatal error: > >> gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) > >> > >> Any comment is highly appreciated. > >> Regards, > >> Alex > > > > > > -- > == > > 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] Fwd: gmx trjcat
On 10/28/19 6:26 AM, Paul bauer wrote: Hello, this looks like a case of misleading documentation. Can you file an issue for this please on redmine.gromacs.org? So that we don't forgot to fix this for the next patch release? A possible work around for you can be that you first convert your files to e.g. XTC format, use trjcat to combine them and convert them back to GRO. Out of curiosity, why was this file format removed as an input for trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB files to make a psuedo-trajectory for ensemble analysis was rather handy. Converting to an intermediate binary format is a workaround, but why add the extra step? Did the trjcat code need de-complicating? -Justin Cheers Paul On 27/10/2019 19:47, Alex wrote: Any comment on this, please? Thanks -- Forwarded message - From: Alex Date: Sat, Oct 26, 2019 at 9:38 AM Subject: gmx trjcat To: Dear all, I want to concatenate some gro file to have a trr or xtc trajectory file out of them as gro files are also acceptable as input files, according the gmx trjcat man page; Options to specify input files: -f [<.xtc/.trr/...> [...]] (traj.xtc) Trajectory: xtc trr cpt *gro* g96 pdb tng So, I fed the .gro files in as input files likes; gmx trjcat -f c*.gro -o trajout.trr However, I get below error that; Fatal error: gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) Any comment is highly appreciated. Regards, Alex -- == 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] NVT equilibration of protein on membrane surface
On 10/28/19 3:27 AM, Olga Press wrote: Prof. Justin thanks so much for the explanation. Why this phenomenon was not observed during the NVT equilibration when I run a simulation of embedded protein? A protein alone in water is surrounded by an isotropic medium that does not exhibit the same differences (anisotropy) in forces that are inherent to membranes. Do two equilibrations of NPT assemble, first with position restraint on the protein (50ns) and second without restains (about 200ns) will be sufficient to fix the problem? You should be able to resolve the bubble faster than that. -Justin Thanks a lot Olga בתאריך יום א׳, 27 באוק׳ 2019 ב-20:45 מאת Justin Lemkul <jalem...@vt.edu >: On 10/27/19 1:20 PM, Olga Press wrote: Prof. Justin thank you for replay. The leaflets are not simply separating, the membrane is deformed and resembles a "chromosome". The image is in the following URL: https://spaces.hightail.com/space/8l6z0Tncyv/files/fi-f3882907-6f37-4230-8c12-40b1f7b1ef22/fv-41ef812d-a030-412f-890f-677af406ebe6/on%20DOPC.JPG The protein is on the DOPC surface, that's why I'm not sure about the setting of the .mdp file. I used the same .mdp settings for the membrae-protein system, where the protein is embedded in a membrane. I would be very grateful if you can help me with that. What you're observing is exactly what I was talking about. It's a bubble in the membrane, leading to the separation of the leaflets. This comes from in adequate water to fill the volume of the unit cell; the waters (which diffuse much faster than the lipids) rush to fill void space and equilibrate their density, but since the ensemble is NVT, the box cannot change size, leaving voids where the waters were. The lipids expand to fill the voids (the polar head groups are drawn to the waters more strongly than the lipid tails are held together) and you get a bubble. Continuing with a sufficiently long NPT relaxation will fix this. -Justin Best regards, Olga בתאריך יום א׳, 27 באוק׳ 2019 ב-18:04 מאת Justin Lemkul < jalem...@vt.edu >: On 10/27/19 11:10 AM, Olga Press wrote: Dear Gromacs users, I run 10ns NVT equilibration with position restains (on the protein) for a system in which the protein is on the membrane surface. I used the following .mdp file title = NVT equilibration for p1-DOPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 500 ; 0.002ps * 500 = 1 ps=10ns dt = 0.002 ; 2 fs ; 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 = 1 nstcalcenergy= 100 nstenergy= 1000 ; Output frequency and precision for .xtc file nstxout-compressed = 1 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 = ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = h-bonds ; H bonds constrained fit to charmm36 ff lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier= force-switch ; same as vfswitch rvdw-switch = 1.0 rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat *tc-grps = Protein DOPC SOL_SOD_CLA* ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 310.15 310.15 310.15 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= no; Do not apply dispertion correction for bilayers by using charmm36 ff ; Velocity generation gen_vel = yes ; assign
Re: [gmx-users] defining parameters in a separate itp file
On 10/27/19 9:24 PM, Dave M wrote: Hi All, I am trying to define a bond between two molecules. Their parameters are defined in separate itp files: molA.itp and molB.itp. I know I can combine both the itp files but I am just wondering if I can define extra bonds/angles joining two molecules in a separate itp file taking care of atom numbers. To test it I defined an extra bond joining two atoms (elastic bond) from two molecules in a separate bond.itp file but it does not look like molecules come close at all. Not sure this is a correct way. And, also is there a way I can print the bond parameters from tpr file to confirm whether all the bonds and angles are read from itp files. My top file looks like this #include "mol1.itp" #include "mol2.itp" #include "bond.itp" [ system ] test [ molecules ] ; namenumber molA 1 molB 1 You don't even need a separate .itp file. After you define [molecules], you can add an [intermolecular_interactions] directive like so: [intermolecular_interactions] [bonds] atom_i atom_j b0 kb Note that atom_i and atom_j, unlike individual [moleculetype] definitions, refer to the global atom numbers in the coordinate file. -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] Fatal Error when launching gromacs 2019.2 on GPU.
Hi, Thanks, setting this variable allowed me to start GROMACS without errors using the CPU. The problem is that this method prevents me from using other free GPUs on the host, but I would like to do this. I also found out that setting the CUDA_VISIBLE_DEVICE variable to available GPUs at the time of launch allows us to solve this problem. Artem On Sat, Oct 26, 2019 at 1:50 AM Szilárd Páll wrote: > Hi, > > This is an issue in one of pre-detection checks that trips due to > encountering exclusive / prohibited mode devices. > > You can work around this by entirely disabling the detection using the > GMX_DISABLE_GPU_DETECTION environment variable. > > Cheers, > -- > Szilárd > > > On Thu, Oct 17, 2019 at 5:01 PM Artem Shekhovtsov < > job.shekhovt...@gmail.com> > wrote: > > > Hello! > > Problem: The launch of mdrun that does not require video cards exit with > > fatal error if at least one video card is busy on the host at that time. > > gmx mdrun -deffnm test -ntmpi 1 -ntomp 1 -nb cpu -bonded cpu > > --- > > Program: gmx mdrun, version 2019.2 > > Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) > > > > Fatal error: > > cudaFuncGetAttributes failed: all CUDA-capable devices are busy or > > unavailable > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > > I have this error in gromacs version 2019.2, 2019.3, 2020.beta. > > Version - 2018.6 is not affected. > > All version builds with the same flags. > > > > Archive with log files and gromacs build files > > > > > https://drive.google.com/file/d/1ahn7S69CU5yvAPlLWHryXmMzcGfdWVxP/view?usp=sharing > > > > > > I would appreciate any help. > > > > Thanks, > > Artem Shekhovtsov. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)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] Reg: GPU use
Dear Bidhan Chandra Garain, Please share the log files of your benchmarks, that will help us better identify if there is an issue and what the issue is. Thanks, -- Szilárd On Mon, Oct 28, 2019 at 8:51 AM Bidhan Chandra Garain wrote: > Respected Sir, > In my lab we have recently installed a GPU Tesla V-100-PCIE, and installed > gromacs-2018.4. I tried to check its performance. I ran a job 128 dmpc > lipid simulation with 23453 atom in my lab cpu with 4 processor with 2 > threading in each processor. There it's performance is ~8 ns/day. But when > the same job I tried to run in gpu using the following command gmx_mpi > mdrun -v -deffnm npt -nb gpu, not only it is taking 40 cpu processors but > also it is very slow. Performnce is ~1 ns/day. Can you please suggest me > why is it taking the 40 cpu processors and how to get the maximum > performance? > > Thanking you in advance. > > Sincerely, > Bidhan Chandra Garain > Ph.D. Student, JNCASR > Bangalore, India > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] error in Umbrella sampling
Hi, Without any information about the parameters you are using in your simulation, no one will be able to provide much help. I recommend reading and understanding this tutorial before you try to perform an umbrella simulation totally blind: http://www.mdtutorials.com/gmx/umbrella/index.html The error is exactly what it says it is. The distance between your pull groups cannot be larger than 0.49 times the box size in one of the dimensions you are pulling because Gromacs calculates the pull distance taking periodic boundary conditions into account. Therefore, if you pull farther than half the box length, the COM distance will be calculated between one of your groups in the simulation box and a group's periodic image in the adjacent periodic cell... and that distance no longer makes any physical sense. This and more are explained in the link given above. Best, John > Dear all,, > I am performing Umbrella sampling on a beeta-sheet to > determine the binding energy between them. I got the following error. > Fatal error: > Distance between pull groups 1 and 2 (4.908636 nm) is larger than 0.49 > times > the box size (4.908511). > while the box-length after equilibratin is > 9.99217 3.99687 5.99530 > I am doing umbrella sampling for the first time. Therefore, I am not able > to understand the error thrown by mdrun. Any help will be 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Fwd: gmx trjcat
Hello, this looks like a case of misleading documentation. Can you file an issue for this please on redmine.gromacs.org? So that we don't forgot to fix this for the next patch release? A possible work around for you can be that you first convert your files to e.g. XTC format, use trjcat to combine them and convert them back to GRO. Cheers Paul On 27/10/2019 19:47, Alex wrote: Any comment on this, please? Thanks -- Forwarded message - From: Alex Date: Sat, Oct 26, 2019 at 9:38 AM Subject: gmx trjcat To: Dear all, I want to concatenate some gro file to have a trr or xtc trajectory file out of them as gro files are also acceptable as input files, according the gmx trjcat man page; Options to specify input files: -f [<.xtc/.trr/...> [...]] (traj.xtc) Trajectory: xtc trr cpt *gro* g96 pdb tng So, I fed the .gro files in as input files likes; gmx trjcat -f c*.gro -o trajout.trr However, I get below error that; Fatal error: gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) Any comment is highly appreciated. Regards, Alex -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error in Umbrella sampling
Dear all,, I am performing Umbrella sampling on a beeta-sheet to determine the binding energy between them. I got the following error. Fatal error: Distance between pull groups 1 and 2 (4.908636 nm) is larger than 0.49 times the box size (4.908511). while the box-length after equilibratin is 9.99217 3.99687 5.99530 I am doing umbrella sampling for the first time. Therefore, I am not able to understand the error thrown by mdrun. Any help will be 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] Reg: GPU use
Respected Sir, In my lab we have recently installed a GPU Tesla V-100-PCIE, and installed gromacs-2018.4. I tried to check its performance. I ran a job 128 dmpc lipid simulation with 23453 atom in my lab cpu with 4 processor with 2 threading in each processor. There it's performance is ~8 ns/day. But when the same job I tried to run in gpu using the following command gmx_mpi mdrun -v -deffnm npt -nb gpu, not only it is taking 40 cpu processors but also it is very slow. Performnce is ~1 ns/day. Can you please suggest me why is it taking the 40 cpu processors and how to get the maximum performance? Thanking you in advance. Sincerely, Bidhan Chandra Garain Ph.D. Student, JNCASR Bangalore, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] NVT equilibration of protein on membrane surface
Prof. Justin thanks so much for the explanation. Why this phenomenon was not observed during the NVT equilibration when I run a simulation of embedded protein? Do two equilibrations of NPT assemble, first with position restraint on the protein (50ns) and second without restains (about 200ns) will be sufficient to fix the problem? Thanks a lot Olga בתאריך יום א׳, 27 באוק׳ 2019 ב-20:45 מאת Justin Lemkul <jalem...@vt.edu >: > > > On 10/27/19 1:20 PM, Olga Press wrote: > > Prof. Justin thank you for replay. > > The leaflets are not simply separating, the membrane is deformed and > > resembles a "chromosome". > > The image is in the following URL: > > > https://spaces.hightail.com/space/8l6z0Tncyv/files/fi-f3882907-6f37-4230-8c12-40b1f7b1ef22/fv-41ef812d-a030-412f-890f-677af406ebe6/on%20DOPC.JPG > > > > The protein is on the DOPC surface, that's why I'm not sure about the > > setting of the .mdp file. I used the same .mdp settings for > > the membrae-protein system, where the protein is embedded in a membrane. > > I would be very grateful if you can help me with that. > > What you're observing is exactly what I was talking about. It's a bubble > in the membrane, leading to the separation of the leaflets. This comes > from in adequate water to fill the volume of the unit cell; the waters > (which diffuse much faster than the lipids) rush to fill void space and > equilibrate their density, but since the ensemble is NVT, the box cannot > change size, leaving voids where the waters were. The lipids expand to > fill the voids (the polar head groups are drawn to the waters more > strongly than the lipid tails are held together) and you get a bubble. > Continuing with a sufficiently long NPT relaxation will fix this. > > -Justin > > > Best regards, > > Olga > > > > > > > > בתאריך יום א׳, 27 באוק׳ 2019 ב-18:04 מאת Justin Lemkul < > jalem...@vt.edu > > >: > > > >> > >> On 10/27/19 11:10 AM, Olga Press wrote: > >>> Dear Gromacs users, > >>> I run 10ns NVT equilibration with position restains (on the protein) > for > >> a > >>> system in which the protein is on the membrane surface. > >>> I used the following .mdp file > >>> > >>> title = NVT equilibration for p1-DOPC > >>> define = -DPOSRES ; position restrain the protein > >>> ; Run parameters > >>> integrator = md; leap-frog integrator > >>> nsteps = 500 ; 0.002ps * 500 = 1 > >> ps=10ns > >>> dt = 0.002 ; 2 fs > >>> > >>> ; 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 = 1 > >>> nstcalcenergy= 100 > >>> nstenergy= 1000 > >>> ; Output frequency and precision for .xtc file > >>> nstxout-compressed = 1 > >>> 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 = > >>> ; Bond parameters > >>> continuation= no; first dynamics run > >>> constraint_algorithm = lincs; holonomic constraints > >>> constraints = h-bonds ; H bonds constrained > fit > >>> to charmm36 ff > >>> lincs_iter = 1 ; accuracy of LINCS > >>> lincs_order = 4 ; also related to accuracy > >>> ; Neighborsearching > >>> ns_type = grid ; search neighboring grid cels > >>> nstlist = 5 ; 10 fs > >>> cutoff-scheme = Verlet > >>> vdwtype = cutoff > >>> vdw-modifier= force-switch ; same as vfswitch > >>> rvdw-switch = 1.0 > >>> rlist = 1.2 ; short-range neighborlist cutoff (in > nm) > >>> rcoulomb= 1.2 ; short-range electrostatic cutoff (in > >> nm) > >>> ; Electrostatics > >>> coulombtype = PME ; Particle Mesh Ewald for long-range > >>> electrostatics > >>> pme_order = 4 ; cubic interpolation > >>> fourierspacing = 0.12 ; grid spacing for FFT > >>> ; Temperature coupling is on > >>> tcoupl = V-rescale ; modified Berendsen > >> thermostat > >>> *tc-grps = Protein DOPC SOL_SOD_CLA* ; three coupling > >> groups - > >>> more accurate > >>> tau_t = 0.1 0.1 0.1 ; time constant, in ps > >>> ref_t = 310.15 310.15 310.15 ; reference > temperature, > >>> one for each group, in K > >>> ; Pressure coupling is off > >>> pcoupl = no; no pressure coupling in NVT > >>> ; Periodic boundary conditions > >>> pbc = xyz
