Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 3
Dear Friends, While performing simulation on our protein of interest, if we want to know the overall charge on our protein then how can we check the same and proceed further for addition of ions to make the system neutral. Regards *Amitabh Jayaswal* *PhD Bioinformatics Scholar* *Banaras Hindu University* *Varanasi, U.P., India | PIN-221005* *+* *City Coordinator* *United Nations* *Rio+22 Power India Program* M: +91 (9868 330088 and 7376 019 155) On Sat, Jul 1, 2017 at 10:50 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: gmx wham problem (edesantis) >2. MDrun -maxh option (Akshay) >3. Re: MDrun -maxh option (Mark Abraham) >4. Re: MDrun -maxh option (Mark Abraham) >5. Checkpoint files error (Apramita Chand) >6. Regarding grid spacing (Apramita Chand) > > > -- > > Message: 1 > Date: Sat, 01 Jul 2017 14:01:42 +0200 > From: edesantis > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx wham problem > Message-ID: <4169af7892add52b5bbaa784647f9...@imap.roma2.infn.it> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear Matthew, > thanks for your opinion. > How can you establish if the histograms are sufficiently overlapped? Is > there any thumbs role? > For what concern the negative sign of reaction coordinates, I think it > could derive from the choice of the order of the pulling groups and the > vector along you are pulling. > > Thank you again > Best regards, > Emiliano > > > On 2017-06-28 17:49, Thompson, Matthew White wrote: > > It looks like you need to sample more states, 13 is not enough. > > Probably more like 20-30+ would be needed to get a smooth PMF as is > > discussed in that tutorial. The weird features in your PMF are from > > insufficiently overlapping histograms, for example the bump near -2.2 > > nm corresponds to having no histogram there. You also see that you > > only have one state near -1.2 nm, so that is probably not being > > sampled enough for WHAM to produce meaningful results. > > > > Also I don't understand the meaning of negative distance as a reaction > > coordinate. If that is the distance between two things, maybe it > > should be positive. It makes it difficult to understand which values > > correspond to them being close and far away. > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of > > edesantis [edesan...@roma2.infn.it] > > Sent: Wednesday, June 28, 2017 10:26 AM > > To: Gmx users > > Subject: [gmx-users] gmx wham problem > > > > dear all, > > > > I am studying the affinity between an antibody and an amyloid peptide; > > I > > am interested in the evaluation of the PMF. I have a problem with the > > PFM shape. > > I followed the protocol described in the umbrella-sampling tutorial > > (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx- > tutorials/umbrella/01_pdb2gmx.html) > > Here below there is the .mdp part for the pulling > > ; Pull code > > pull= yes > > pull_ngroups= 2 > > pull_ncoords= 1 > > pull_group1_name= Chain_Abeta > > pull_group2_name= Chains_Antibody > > pull_coord1_type= umbrella ; harmonic biasing force > > pull_coord1_geometry= direction > > pull_coord1_groups = 1 2 > > pull_coord1_vec = 38.207 68.611 29.8493 > > pull_coord1_rate= 0.002; 0.01 nm per ps = 10 nm per ns > > pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 > > pull_coord1_start = yes ; define initial COM distance > > > 0 > > > > After the pulling simulation, I?ve extracted 13 configuration; for each > > them, 36 ns of equilibration were performed. These are the mdp > > directives: > > ; Pull code > > pull= yes > > pull_ngroups= 2 > > pull_ncoords= 1 > > pull_group1_name= Chain_Abeta > > pull_group2_name= Chains_Antibody > > pull_coord1_type= umbrella ; harmonic biasing force > > pull_coord1_geometry= direction > > pull_coord1_groups = 1 2 > > pull_coord1_vec = 38.207 68.611 29.8493 > > pull_coord1_rate= 0.00 > > pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Re: [gmx-users] Nano-structures equilibration
Thank you very much, Alex. I also performed the process on GPU, and I got the below error: step 1: Water molecule starting at atom 96743 can not be settled.Check for bad contacts and/or reduce the timestep if appropriate.Wrote pdb files with previous and current coordinates WARNING: Listed nonbonded interaction between particles 4321 and 4328at distance 21.231 which is larger than the table limit 1.853 nm. This is likely either a 1,4 interaction, or a listed interaction insidea smaller molecule you are decoupling during a free energy calculation.Since interactions at distances beyond the table cannot be computed,they are skipped until they are inside the table limit again. You willonly see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there isprobably something wrong with your system. Only change the table-extensiondistance in the mdp file if you are really sure that is the reason. I would appreciate any help. Regards,Mohammad From: Alex To: gmx-us...@gromacs.org Sent: Friday, 30 June 2017, 22:21:26 Subject: Re: [gmx-users] Nano-structures equilibration You have performance-related errors, maybe try a different number of ranks, or another machine, or OpenMP instead of MPI -- hope others will be able to comment on technical issues. Your question was whether you should abandon nanostructure equilibration because of this -- the answer is of course no. Alex On 6/30/2017 5:03 AM, Mohammad Roostaie wrote: > I asked it since I got some errors regarding the NPT equilibration, > also this link says that turn off the pressure coupling. > > The errors which I received is as follow: > > 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 > —---— > > Halting parallel program mdrun_mpi on rank 0 out of 14 > — > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > > Furthermore, I used -dd (with the values of 7 2 1) option, and I got > this error: > > Fatal error: > 1130 particles communicated to PME rank 14 are more than 2/3 times the > cut-off out of the domain decomposition cell of their charge group in > dimension y. > This usually means that your system is not well equilibrated. > For more information and tips for troubleshooting, please check the > GROMACS > website at Errors - Gromacs > > Regards, > M > > > On Friday, June 30, 2017, 12:47:05 PM GMT+4:30, Alex > wrote: > > > Is this a philosophical question? Yes, it is certainly possible for > graphene+peptide to exist in water under pressure. > > > On 6/30/2017 12:05 AM, Mohammad Roostaie wrote: > > Hi All, > > Is it possible and necessary to run NPT equilibration process on the > nanostructure systems (graphene+peptide in water)? Since I got some > errors regarding this process. > > Regards,Mohammad > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] How to convert amber prep and param file to gromac topology file
Hi everyone I have prep and param file for hem.o2 I want to know how I can convert it to itp file thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] can i produce the NO force files for system
hi everyone can i produce the force field for NO nitric oxide that bonded with heme Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding grid spacing
Dear All, Which is more appropriate fourier grid spacing for gromos53a6 ff with cutoffs being 0.9 and 1.4nm? 0.16 or 0.12?? I've not seen too many papers with 0.16 being used for this forcefield and that too with cutoffs like 1.0 for rcoulomb and rvdw. Is there any problem if I use fourier spacing of 0.16 with these cutoffs(0.9,1.4)? Also,should the grid spacing be same for equilibration and production runs?? Yours sincerely, Apramita -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Checkpoint files error
Dear All, After equilibration, I want to pass on the checkpoint files state.cpt for production run for which I give the command g_mdrun -s md.tpr -c md.gro -o md.trr -cpi state.cpt -cpo state_md.cpt The job terminates with error that output files for checkpoint files are insufficient Just 1 out of 3files are present Required: npt.trr ,npt.edr I have the above mentioned files in the folder ,still the error message exists What is the correct procedure to pass checkpoint files? Also,for generation of tpr file,we use .gro files from the last run.what are the advantages of using .cpt files? Are they essential? Thanks in advance for your suggestions Yours sincerely Apramita -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] MDrun -maxh option
Hi, Inter-simulation signalling for coordinating stuff like mdrun -maxh for replica exchange has not had a great history. I believe it finally works properly in 2016, but haven't actually tried it. Mark On Sat, Jul 1, 2017 at 3:45 PM Akshay wrote: > Hello All, > > The cluster of my University uses a queuing system with a maximum wall-time > of 12 hours. So, I run mdrun with the option -maxh 11.9 and subsequently > restart the simulation using the output checkpoint files iteratively. > However, the -maxh option has not been killing the jobs when I run replica > exchange jobs across nodes (4 replicas with 2 nodes for each replica (16 > cores per node)). I only get an output error with the job scheduler killing > the job at the 12 hour mark. > > I would love to have suggestions on how to begin my troubleshooting. Could > it be an installation issue on specific nodes? Or should I reduce the -maxh > value further to allow time for mdrun to write all the checkpoint files? > > Thanks, > Akshay > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] MDrun -maxh option
Hello All, The cluster of my University uses a queuing system with a maximum wall-time of 12 hours. So, I run mdrun with the option -maxh 11.9 and subsequently restart the simulation using the output checkpoint files iteratively. However, the -maxh option has not been killing the jobs when I run replica exchange jobs across nodes (4 replicas with 2 nodes for each replica (16 cores per node)). I only get an output error with the job scheduler killing the job at the 12 hour mark. I would love to have suggestions on how to begin my troubleshooting. Could it be an installation issue on specific nodes? Or should I reduce the -maxh value further to allow time for mdrun to write all the checkpoint files? Thanks, Akshay -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] gmx wham problem
Dear Matthew, thanks for your opinion. How can you establish if the histograms are sufficiently overlapped? Is there any thumbs role? For what concern the negative sign of reaction coordinates, I think it could derive from the choice of the order of the pulling groups and the vector along you are pulling. Thank you again Best regards, Emiliano On 2017-06-28 17:49, Thompson, Matthew White wrote: It looks like you need to sample more states, 13 is not enough. Probably more like 20-30+ would be needed to get a smooth PMF as is discussed in that tutorial. The weird features in your PMF are from insufficiently overlapping histograms, for example the bump near -2.2 nm corresponds to having no histogram there. You also see that you only have one state near -1.2 nm, so that is probably not being sampled enough for WHAM to produce meaningful results. Also I don't understand the meaning of negative distance as a reaction coordinate. If that is the distance between two things, maybe it should be positive. It makes it difficult to understand which values correspond to them being close and far away. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of edesantis [edesan...@roma2.infn.it] Sent: Wednesday, June 28, 2017 10:26 AM To: Gmx users Subject: [gmx-users] gmx wham problem dear all, I am studying the affinity between an antibody and an amyloid peptide; I am interested in the evaluation of the PMF. I have a problem with the PFM shape. I followed the protocol described in the umbrella-sampling tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html) Here below there is the .mdp part for the pulling ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_Abeta pull_group2_name= Chains_Antibody pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= direction pull_coord1_groups = 1 2 pull_coord1_vec = 38.207 68.611 29.8493 pull_coord1_rate= 0.002; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 After the pulling simulation, I’ve extracted 13 configuration; for each them, 36 ns of equilibration were performed. These are the mdp directives: ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_Abeta pull_group2_name= Chains_Antibody pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= direction pull_coord1_groups = 1 2 pull_coord1_vec = 38.207 68.611 29.8493 pull_coord1_rate= 0.00 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Then I ran the wham command: Gmx wham –it list_tpr.dat –if list_pullf.dat -v –b 2 –o –hist And I’ve obtained the following pictures: http://i66.tinypic.com/11t5zdv.png http://i67.tinypic.com/30u8g8x.png Do you have any idea of why the pfm profile has this strange shape? Could it come from any kind of error I’ve made during the simulations? If there are not errors, it seems that the configurations in which the peptide is far from the antibody are more energetically favoured respect to those in contact with the antibody, but I have some doubts about it… Can you help me? Thank you in advance, best regards, Emiliano -- Emiliano De Santis -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Emiliano De Santis -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] replica exchange
Hi, Your problem is external to GROMACS, so please follow up e.g. with your system administrators. My guess is that your PATH does not include mdrun_mpi (so you should source GMXRC correctly), or that you need to specify its full path when you tell mpirun to run it. Mark On Sat, Jul 1, 2017 at 8:59 AM Neda Rafiee wrote: > Dear All, > I am doing replica exchange for a peptide in water and I used the > following command to run my system: > mpirun -np 4 mdrun_mpi -v -multidir equil[0123] > but I encountered with an error saying: > HYDU_create_process (utils/launch/launch.c:75): execvp error on file > mdrun_mpi (No such file or directory) > Can anyone help me find out the problem? > Thanks > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
