Re: [gmx-users] why it is so slow in Blue gene?
On 25/04/2012 3:24 PM, Albert wrote: hello: it is blue gene P. And the gromacs is single precision in the cluster. Getting Loaded...And the administrator told me that I have to use the multiples of 32 in the bg_size parameter. The number specified in -np should be 4 times bg_size. Yes, but your system is too small to make use of 128 processors. Also, get rid of -launch and -nt from your command line, since they do nothing. It is even slower than my own workstation with 16 core. here is the log file I get: No, that's the stdout file. Look at the end of the .log file. -log Reading file npt_01.tpr, VERSION 4.5.5 (single precision) Loaded with Money Will use 112 particle-particle and 16 PME only nodes This is guaranteed to lead to woeful performance with your .mdp settings, but you will have to look towards the beginning of the .log file to find out why mdrun selected this. Odds are good that your system size is so small that the minimum particle-particle cell size (constrained by rcoulomb) doesn't give mdrun any good options that use all the processors. You'd likely get better raw performance with twice the number of atoms or half the number of processors. Mark This is a guess, check the performance at the end of the log file Making 3D domain decomposition 4 x 4 x 7 starting mdrun 'GRowing Old MAkes el Chrono Sweat' 50 steps,500.0 ps. step 0 vol 0.64! imb F 16% pme/F 0.22 step 100, will finish Wed Apr 25 18:28:06 2012 vol 0.65! imb F 17% pme/F 0.21 step 200, will finish Wed Apr 25 18:09:54 2012 vol 0.67! imb F 18% pme/F 0.21 step 300, will finish Wed Apr 25 18:03:12 2012 vol 0.69! imb F 18% pme/F 0.21 step 400, will finish Wed Apr 25 17:58:25 2012 vol 0.67! imb F 19% pme/F 0.21 step 500, will finish Wed Apr 25 17:55:26 2012 vol 0.68! imb F 19% pme/F 0.22 step 600, will finish Wed Apr 25 17:53:31 2012 vol 0.68! imb F 19% pme/F 0.22 step 700, will finish Wed Apr 25 17:51:57 2012 vol 0.68! imb F 19% pme/F 0.22 step 800, will finish Wed Apr 25 17:50:32 2012 vol 0.68! imb F 20% pme/F 0.22 step 900, will finish Wed Apr 25 17:49:14 2012 vol 0.67! imb F 21% pme/F 0.22 step 1000, will finish Wed Apr 25 17:48:13 2012 vol 0.68! imb F 20% pme/F 0.22 step 1100, will finish Wed Apr 25 17:47:28 2012 vol 0.67! imb F 21% pme/F 0.22 step 1200, will finish Wed Apr 25 17:46:50 2012 vol 0.67! imb F 21% pme/F 0.22 step 1300, will finish Wed Apr 25 17:46:15 2012 On 04/24/2012 06:01 PM, Hannes Loeffler wrote: On Tue, 24 Apr 2012 15:42:15 +0200 Albertmailmd2...@gmail.com wrote: hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for You don't give any information what exact system that is (L/P/Q?), if you run single or double precision and what force field you are using. But for a similar sized system using a united atom force field in single precision we find about 4 ns/day on a BlueGene/P (see our benchmarking reports on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx). I would expect a run with the CHARMM 27 force field in double precision to be roughly 3 times slower. We found scaling to 128 cores to be reasonably good. Also, check our report for problems when compiling with higher optimisation. Hannes. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Error: coordinate file does not match with the topology file
Please do not make unsolicited general GROMACS inquiries to private email addresses. The mailing lists exist for these kinds of purposes. On point, you cannot be helped unless you provide the command lines that you used and describe the objectives you were trying to achieve. Whatever changes you make to one of the coordinate and .top file must be matched in the other. Mark Original Message Subject:Error: coordinate file does not match with the topology file Date: Wed, 25 Apr 2012 02:05:45 +0800 (SGT) From: sonali shinde shindesonal...@yahoo.co.in Reply-To: sonali shinde shindesonal...@yahoo.co.in To: mark.abra...@anu.edu.au mark.abra...@anu.edu.au - Forwarded Message - *From:* sonali shinde shindesonal...@yahoo.co.in *To:* vini k vineetha_mand...@yahoo.co.in *Sent:* Monday, 23 April 2012 6:48 PM *Subject:* Error: coordinate file does not match with the topology file Dear Sir, I am a user of gromacs 4.0 for molecular dynamic study of a protein molecule. I have generated trajectory file before using the same commands that I use now. Recently I am suffering some problem using Gromacs , my coordinate file does not matches with the topology file.I have attached the pdb file protein, .gro and .top file . I have encountered same error a number of times with three different proteins.Please suggest the answer for the same. Thanking you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to increase the ratio of cell size to constrain length per error message
On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am using gromacs version is 4.5.3.and running my jobs on single node with 8 cores. I have two different systems which contain about 425000 atoms (protein + Lipid +SOL) one with bound ligand and another one unbound protein.I have successfully reached up to NPT equilibration run step, It is a poor idea to do equilibration with Parinello-Rahman, which is unstable when the system is not already close to equilibrium. For some reason people still do it, despite at least a post per week on this list suggesting against it, and a warning in the manual. Use Berendsen to fix the density, then equilibrate further with P-R to get the right ensemble. now I want to continue the same for production run. Without ligand I am able to run successfully But the same system with ligand is crashing with following error- D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are are connected via constraints from the neighbouring cells This probably means your constraint length are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs_order. I'd rather expect your system was blowing up because of the above issue. Perhaps the suggestion in the error message is not as complete as could be desired - you have so many atoms per processor that the constraint length would normally be tiny with respect to the cell size. So I think the things you have tried below are rearranging the deck chairs on the Titanic. Mark Accordingly following the suggestions given in the error I tried to solve it with Following log file and changed, 1.1. -rcon Estimated maximum distance required for p-lincs was 0.877 thus I increased it to 0.900 then it thrown another error. The initial cell size (0.877) is smaller than the cell size limit (0.900) 2 .Then I tried to increase the --dds and --rdd from original values of 1.25 and 0.623 to 1.30 and 0.670 respectively. But it does not help and ended with run crash. /*What I did was logical or I did it wrongly?*/ /*Now can anyone please suggest me the appropriate way to deal with the problem mentioned above? */ As I want the continuation of the same run without altering the output after change in the parameters (As I have to compare the output with unbound protein run thus can't afford change in output with change in parameters) I know that I need to change some of the parameters in .mdp file such as fourierspacing from 0.16 to 0.12 and on the contrary increase the pme_order from say 4 to 6. /*But as asked above by doing so the output will not or will be the exact continuation run?*/ /*How to increase the ratio of cell size to constrain length per error message?*/ /*If any better way of doing so without changing the output please suggest,*/ I am suffering from the same problem since long, Please help me .Please see the mdp file for the reference. integrator= md nsteps = 1000 dt = 0.002 ; 2 fs ; Output control nstxout= 1000; nstvout = 1000; nstxtcout = 1000; nstenergy= 1000; nstlog = 1000; ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 5 rlist= 1.2 rcoulomb= 1.2 rvdw= 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps= Protein PSOL_NA_CL ; tau_t= 0.5 0.5 0.5 ref_t= 323 323 323 group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; pcoupltype = semiisotropic tau_p = 2.0 ; time ref_p = 1.0 1.0 ; reference compressibility = 4.5e-5 4.5e-5 ; ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel = no Thanking in Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list.
Re: [gmx-users] Can I equilibrate with Parinello-Rahman?
On 26/04/2012 10:47 PM, PAVAN PAYGHAN wrote: Dear Mark, Thanks a lot for the reply and highlighting the cause of error that I was facing. Still can it be possible to overcome the same error with the available facility. Unfortunately you're forcing me to guess the context for this question. If there was a way to make P-R P-couping stable for equilibration in general, then it would not have the reputation for being unstable... I gave my advice about what to do already. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors
On 27/04/2012 3:53 PM, seera suryanarayana wrote: Respected sir, While i am running the gromacs software i am getting the following error.Kindly tell me how to over come the error. Fatal error: Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms while sorting atoms. Please check out http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette for advice on how to construct effective requests for help. With only the above information, all that can be said is that the tool you were using expected residue LYS that was first in some sequence, and that was being mapped to .rtp entry LYSH, to lack atom an atom named HA. Background information on the required matching can be found in chapter 5 of the manual. Details of how the mismatch occurred can only be found in the files you have constructed. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors
On 27/04/2012 5:07 PM, seera suryanarayana wrote: Respected Sir, While i am running the gromacs software i am getting the following error.Kindly knowing how to over come the error. Fatal error: Residue 'CCN' not found in residue topology database http://www.gromacs.org/Documentation/Errors Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to use -tablep mdrun option?
On 27/04/2012 11:07 PM, Marcelo Lopez wrote: Hi all, I'm trying to run a coarse grained system with tabulated non-bonding potentials for 3 kind of particles. I need to set all the 1-4 interactions to zero Why not use nrexcl = 3 in your [moleculetype] like the example in manual 5.7.1? (and probably gen-pairs = no for your force field) but I can't find in the manual or elsewhere hot to construct the tables for the -tablep option of mdrun. Searching the manual text for tablep finds me information in section 7.3, which strongly suggests the information in 6.7.2 is applicable. I've readed a thread in the mailing list but still the information I get is uncomplete... (the manual says absolutely NOTHING!) 1) In these tables, do I specify the index number of every 1-4 pair or only the labes of the groups involved? Followed by the C6 and C12 parameters. Only a functional form is specified in the table. Topology (which 1-4 pairs exist) is entered in the .top file. Parameters (charge, C6 and C12) likewise. Go and look at 6.7.2 and the example tables in your GROMACS distribution. For example, for the atom index 1 and 5 (energy groups A and B), one tablep*.xvg file must contain this 1 5 0.0 0.0 or this (valid for all the AB 1-4 pairs?)? AB0.00.0 I ask... And still something is missing? The system has no charges, do I say this too in every tablep*.xvg file? how? Charges are specified in the [atoms] section of your [moleculetype]. If they're zero, then nothing will ever be computed from them, so you can probably use anything you like with the the f() part of the tabulated potentials. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD - low temperature ranges
On 27/04/2012 10:59 PM, Tomek Wlodarski wrote: Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources and I am wondering if for studing 175 aa protein is better to start from 250K and up to 350 K or choose from 300-400K (just an example) Depends on the temperature(s) at which you wish to make observations. Sampling is normally enhanced at higher temperatures, so unless you want the ensemble at some low temperatures, it is normal to start at your lowest observation temperature. Of course, you could always read the reasoning provided by the authors in their paper, or email them for clarification... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF
On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file. Does setting gen_pairs to yes in the [defaults] section in the forcefield.itp work? Probably. What documentation exists is probably in the walk-through example of manual 5.7.1. You can probably construct yourself a trivial test case if you wish to verify how things work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to use -tablep mdrun option?
On 28/04/2012 12:19 AM, Marcelo Lopez wrote: Thank you very much Mark, I have already in my topology files nrexcl = 3 and gen-pairs = no Please enlight me... Does this mean that all the 1-4 interactions (I have tabulated bonds, angles and dihedrals) are zero? Look at what the .log file reports for energies (or the .edr file). If there are no named 1-4 terms, then there are no 1-4 interactions. grompp might report this also. gmxdump on your .tpr does allow you to probe this (but not as easily as checking the .log file). Because I'm trying to put a strong repulsive part in the non-bonding potentials and the energy grows to Inf. That may or may not have anything to do with 1-4 interactions, but is reasonably likely to be problematic without careful parameterization. Also, you haven't said what energy grows without bound, so it's hard to know how this relates to the foregoing. Mark Thanks. Marcelo Lopez El día 27 de abril de 2012 10:38, Mark Abraham mark.abra...@anu.edu.au escribió: On 27/04/2012 11:07 PM, Marcelo Lopez wrote: Hi all, I'm trying to run a coarse grained system with tabulated non-bonding potentials for 3 kind of particles. I need to set all the 1-4 interactions to zero Why not use nrexcl = 3 in your [moleculetype] like the example in manual 5.7.1? (and probably gen-pairs = no for your force field) but I can't find in the manual or elsewhere hot to construct the tables for the -tablep option of mdrun. Searching the manual text for tablep finds me information in section 7.3, which strongly suggests the information in 6.7.2 is applicable. I've readed a thread in the mailing list but still the information I get is uncomplete... (the manual says absolutely NOTHING!) 1) In these tables, do I specify the index number of every 1-4 pair or only the labes of the groups involved? Followed by the C6 and C12 parameters. Only a functional form is specified in the table. Topology (which 1-4 pairs exist) is entered in the .top file. Parameters (charge, C6 and C12) likewise. Go and look at 6.7.2 and the example tables in your GROMACS distribution. For example, for the atom index 1 and 5 (energy groups A and B), one tablep*.xvg file must contain this 1 5 0.0 0.0 or this (valid for all the AB 1-4 pairs?)? AB0.00.0 I ask... And still something is missing? The system has no charges, do I say this too in every tablep*.xvg file? how? Charges are specified in the [atoms] section of your [moleculetype]. If they're zero, then nothing will ever be computed from them, so you can probably use anything you like with the the f() part of the tabulated potentials. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] SWM4_DP water on graphite surface
On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted crazily after a few time step (graphite surface deform critically, blow). The error is Step 140: The charge group starting at atom 266 moved than the distance allowed by the domain decomposition (1.00) in direction Z distance out of cell 1.038218 Old coordinates:0.1232.6276.000 New coordinates:0.0130.671 11.038 Old cell boundaries in direction Z:5.978 10.000 New cell boundaries in direction Z:5.660 10.000 --- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 3654 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I don't understand why I freeze the graphite surface but the carbon atom moved around. If it is because of bad contact, I think the water should be blown instead of carbon atom I ran the SPC/E water model on graphite very well. Probably you didn't use freezedim on the SOL degrees of freedom when you used that water model, as you have here. Mark I attached the mdp file, the topology file. Please let me know if I did anything wrong. Thanks in advance. Tuan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] SWM4_DP water on graphite surface
On 28/04/2012 10:54 AM, Ho, Tuan A. wrote: Thank Mark, I freeze the SOL because I would like to check if it is because of SOL bad contact. You can't do a dynamical simulation with zero degrees of freedom. However, it turns out that the graphite deformation is the problem. Under what conditions? Your earlier simulation probably blew up because of the above. Mark My friend asks me to use only one processor, and it is running well (no SOL freeze). Hopefully, after I got the final configuration for serial run, I will be able to perform a parallel simulation. Thank you so much. Any idea for this problem is highly appreciated since I am not sure if I will be able to perform a parallel job. Tuan. *From:*gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Mark Abraham *Sent:* Friday, April 27, 2012 6:36 PM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] SWM4_DP water on graphite surface On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted crazily after a few time step (graphite surface deform critically, blow). The error is Step 140: The charge group starting at atom 266 moved than the distance allowed by the domain decomposition (1.00) in direction Z distance out of cell 1.038218 Old coordinates:0.1232.6276.000 New coordinates:0.0130.671 11.038 Old cell boundaries in direction Z:5.978 10.000 New cell boundaries in direction Z:5.660 10.000 --- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 3654 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I don't understand why I freeze the graphite surface but the carbon atom moved around. If it is because of bad contact, I think the water should be blown instead of carbon atom I ran the SPC/E water model on graphite very well. Probably you didn't use freezedim on the SOL degrees of freedom when you used that water model, as you have here. Mark I attached the mdp file, the topology file. Please let me know if I did anything wrong. Thanks in advance. Tuan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] blue gene running error
On 28/04/2012 2:04 PM, Albert wrote: hello: I am running NPT on a blue gene cluster, but the jobs always failed with following messages. However, everything goes well if I run it on my local cluster: Systems with marginally stable initial conditions can do this. See http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] blue gene running error
On 28/04/2012 4:14 PM, Albert wrote: hello Mar: thanks a lot for kind reply. From the link you you mentioned, it seems that this problem comes from the MD system itself. However, it goes well in my workstation. Moreover, I visualized and analyzed the results from my workstation running, everything goes well. I don't find any problem with it. But I don't know why it doesn't work in the blue gene computer. Sometimes a marginally stable calculation will work or not based on apparently insignificant things, like whether it's in parallel or not. Numerical integration can be messy. If you prepare the system slightly better and/or equilibrate more gently, then it will run under BlueGene, from your evidence of what I assume to be lucky good behaviour on your workstation. Mark THX ALbert On 04/28/2012 07:36 AM, Mark Abraham wrote: On 28/04/2012 2:04 PM, Albert wrote: hello: I am running NPT on a blue gene cluster, but the jobs always failed with following messages. However, everything goes well if I run it on my local cluster: Systems with marginally stable initial conditions can do this. See http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] disulfide bonds
On 29/04/2012 7:02 PM, Hagit G wrote: I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb The main problem is: When I use pdb2gmx it adds H atoms to Cys, hence the disulfide bonds are no longer conected after energy minimization. How can I avoid this addition of H atoms? (I tried to make this bond after, but I didn't make it because one Cys is in the long chain and the other one is in the short chain) See http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds about requirements for having atoms (and thus chains) in the same [moleculetype]. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Make an index file
On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title= NVT equilibration for POPC define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 5; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained 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 rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= POPC SOL; two coupling groups - more accurate Here you instruct grompp to expect the POPC group... tau_t= 0.10.1; time constant, in ps ref_t= 323 323; 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= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? ... but POPC is not defined implicitly by your .top+.gro combination, nor explicitly in an index file supplied with grompp -n. AFAIK if your [moleculetype] is named POPC then it is all OK, but maybe the fact that your .gro file has the POPC residues named POP is confusing that mechanism. As you can see with your earlier example with make_ndx, the POP group is defined implicitly by the residue names in your .gro file, so if you use that output index file and reference POP in your .mdp file, all will be good. You might get away without using that index file, but I am not sure about this. Simpler still is to use Water and non-Water as your T-coupling groups, but this will need changing if down the road you need Protein as well (or such). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun
On 30/04/2012 3:38 PM, Anirban Ghosh wrote: On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung adeyo...@andrew.cmu.edu mailto:adeyo...@andrew.cmu.edu wrote: Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to start parallel runs without calling mpirun. So on version 4.5.5, I can start a job on eight CPUs using simply the command: mdrun -s topol.tpr -nt 8 However, now I am using a different node on my department's cluster, and this node instead has Gromacs 4.5.4 (compiled without automatic threading). So, I must use mpirun to start parallel runs. I have tried this command: mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with --enable-mpi option? -Anirban where mymachines is an (extensionless) file containing only the text c60 slots=8. (c60 is the name of the node that I am using.) I get this error message: Missing: program name. Program mdrun either does not exist, is not executable, or is an erroneous argument to mpirun. This is strange, because mdrun is, I think, in my path. For example, if I type mdrun -h, I get the manual page for mdrun (version 4.5.4). Then I tried the command which mdrun, and it gave me this output: /usr/local/gromacs/bin/mdrun So, next I tried to call mdrun via mpirun using the specific path for mdrun: mpirun -machinefile mymachines -np 8 /usr/local/gromacs/bin/mdrun -s topol.tpr This starts running my simulation, but when I look in top, the simulation is only running on a single CPU; there is only one entry for mdrun in top, and it has only %CPU=100 (not eight different entries for mdrun, nor one entry with %CPU=800). Also, the simulation is going at the speed I would expect for running on a single CPU -- it is very slow, so I am convinced that, as top suggests, mdrun is running on only one CPU. Strangely, my colleagues are able to run jobs in parallel using the exact commands that I described above. So apparently something is wrong with my user ID, although there are no error messages (except the error message about Missing: program name that I described). If you have time, do you have any suggestions for other things that I can try? Do you think that something could be wrong with my bashrc file? Get a simple MPI test program and prove how you can run it in parallel. Then worry about GROMACS. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] TRR file with nstxout= 0
On 30/04/2012 6:34 PM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 4/27/12 12:09 PM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 4/27/12 11:34 AM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 4/27/12 11:22 AM, Steven Neumann wrote: Dear Gmx Users, I am running 2 us simulation in implicit solvent model: define= -DPOSRES integrator= sd; leap-frog integrator nsteps= 5 ; 0.004 * 5= 2 us dt= 0.004 ; 4 fs ; Output control nstxout = 0 nstxtcout= 5; xtc compressed trajectory output every 2 ps nstenergy= 1 ; save energies every 2 ps nstlog= 1 ; update log file every 2 ps How come my trajectory (trr) is being created and takes 80 GB? The default for nstvout is 100, so you're likely getting very frequent output of velocities into the .trr file. -Justin Thank you This job crashed due to the quota exceeded. If change my mdp file (with additional nstvout=0) using tpbconv and run it from the checkpoint file it should work then with no trr file? If you need to change the .mdp file, you can't use tpbconv; use grompp to generate a new .tpr file and submit the new job. So if I will create new mdp file (with additional nstvout=0 to get rid of trr files) and use: mdrun -s new.tpr -cpi last.cpt Will I continue from the checkpoint? That's the question I posed below... I'm not sure if you can pick up using mdrun -cpi if the settings have changed, but you can try. Yes you can, from 4.0 you do not have to specify -append just -cpi file if the job crashed. I am aware of checkpointing, but what I'm not sure of is if you change output options (or others) mid-stream, if the checkpointing mechanism will complain, particularly due to the changes in the .trr content. You'll have to try and see. -Justin Indeed, it complains in terms of not present trr file (3 out of 4 files present) and he does not want to carry on. But when I change name of the output it starts from the checkpoint generating new files. Yes, that will be the effect of the (default) mdrun -append yes in 4.5 Can I then somehow connect those two xtc trajectories using trjconv? Yes, or better trjcat. Be sure to read and understand their -h output first. Which tpr file I should use? You don't even need a .tpr file to concatenate trajectory files. Mark Steven -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regading error
On 30/04/2012 7:49 PM, seera suryanarayana wrote: Dear all gromacs users, I tried the grompp and i got the following error.number of coordinates in coordinate file (4INS_b4ion.gro, 90396) does not match topology (4INS.top, 90393). Is there any explanation why is this happens.I would appreceate any help.I am new in using moleculer dynamics and particularly in gromacs. You've been given links with direct information about the particular errors you're seeing. You've been given links that describe preferred ways to construct requests for help that are likely to help you get constructive feedback. Being new doesn't excuse you from learning to search the freely available resources that already exist, rather than expecting others to do it for you ;-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box of water
On 1/05/2012 12:02 PM, cuong nguyen wrote: Dear Gromacs Users, I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10 to create box of 3010 water molecules. However, now I need to create a same size box with only 846 water molecules. Please help me to do this. Use a suitable combination of editconf, genbox and/or genconf. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box of water
On 1/05/2012 12:20 PM, cuong nguyen wrote: Thanks, I tried to add -maxsol 846 to the command and got the box with 846 water molecules. However, when I use VMD to visualize the box, these molecules concentrate on 1/3 the box space. I do need the molecules to spread out whole box. So next time think about asking the question whose answer you actually want... Do some arithmetic and put a suitable box around a single water molecule. Then replicate with genconf, like I suggested last time. Mark Cheers, Cuong 2012/5/1 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 4/30/12 10:02 PM, cuong nguyen wrote: Dear Gromacs Users, I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10 to create box of 3010 water molecules. However, now I need to create a same size box with only 846 water molecules. Please help me to do this. Use the -maxsol option when invoking genbox. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] A problem with gromacs versions
On 1/05/2012 6:49 PM, Shima Arasteh wrote: Dear gmx users, I've installed the gromacs version 4.5.5 on my laptop. But the version of gromacs on the cluster, which I want to run MD, is 4.0. First of all. is it possible that I use this one? Yes, but you will run into differences, such as that below. Get your admins to update for better performance. Mark Secondly, when I run this command, I get a fatal error as below: # grompp -f md.mdp -c npt.gro -t npt.cpt -p popc.top -o md.tpr Fatal error: Invalid dihedral type 9 Is it because of the differences between versions? Thanks in advance, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] disre and posres together?
On 1/05/2012 4:58 PM, Banafsheh Mehrazma wrote: Dear all; I am wondering if we can use both disre and POSRES in .mdp file together? Yes, this is a routine procedure for equilibrating while preserving an initial structure for some reason. To be more perspective, is it correct to add all these below in the *.mdp file? .. define= -DPOSRES disre = simple disre-weighting = equal disre-mixed = no disre-fc = 1000 disre-tau = 0 . That looks fine. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] To know
On 2/05/2012 5:12 PM, Anik Sen wrote: Hi, Am Anik Sen, using gromacs 3.3.2 version. I have a very simple question to ask, In the mdp file, like the emmod.mdp or run.mdp needed for a MD run there are three factors namely,rlist, rcoulomb and rvdw. 1. Is there any minimum value for these three below which the results will be absurd for any system, or we can use any value for these? 2. For a system we are using 0.1. Is this a right one or not? You should be attempting to replicate either the parameter regime under which your force field was developed, or a similar set under which it has been shown to produce results that agree with real observations. Pulling numbers out of the air is not appropriate. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] To know
On 2/05/2012 5:37 PM, Mark Abraham wrote: On 2/05/2012 5:12 PM, Anik Sen wrote: Hi, Am Anik Sen, using gromacs 3.3.2 version. I have a very simple question to ask, In the mdp file, like the emmod.mdp or run.mdp needed for a MD run there are three factors namely,rlist, rcoulomb and rvdw. 1. Is there any minimum value for these three below which the results will be absurd for any system, or we can use any value for these? 2. For a system we are using 0.1. Is this a right one or not? You should be attempting to replicate either the parameter regime under which your force field was developed, or a similar set under which it has been shown to produce results that agree with real observations. Pulling numbers out of the air is not appropriate. And since this is apparently new work, you should upgrade to a more modern GROMACS for much better performance, more useful resources and hopefully fewer bugs! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to remove H atom from residue in gro file?
On 2/05/2012 8:55 PM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a disulfide bond. Gromacs automatically adds H atoms. Although the disulfide bond is there, Gromacs ignore it because *each cystein is on a different chain*. So it adds H and therefor the disulfide bond is ruined during energy minimization. Is there any way to recreate such a disulfide bond (Please don't tell me again about -ss it works only on one chain. Moreover, the bond is existed on the pdf file.) or never ruined it at the first place? Yes, and the clue to how to combine the chains to give the mechanism a chance of working is on the page I linked last time: http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Automation of selecting water around a molecule
On 2/05/2012 7:49 PM, Lara Bunte wrote: Hi I need a little help in using Linux. I wrote this script for the bash, that I called g_select_script.sh: #!/bin/bash g_select -s mol_in_water.pdb -select 'Close to ISO resname SOL and within 0.4 of resname ISO' -on make_ndx -f mol_in_water.pdb -o index2.ndx cat index2.ndx index.ndx index3.ndx make_ndx -f mol_in_water.pdb -n index3.ndx -o index_final.ndx trjconv -n index_final.ndx -f mol_in_water.pdb -s mol_in_water.pdb -o output.pdb After this I make a file called parameters_for_g_select_script, that looks like: 2 q 2|7 q 8 And finally I type in the bash this command: ./g_select_script.sh parameters_for_g_select_script Sadly this does not work. It works correct until make_ndx -f mol_in_water.pdb -n index3.ndx -o index_final.ndx with parameters 2|7 and q The numbers of the groups are correct. I guess, that 2|7 is not transfered correctly. I tried '2|7' and 2|7 that also do not work. What is wrong in my automation? Please help a Linux noob like me. Not sure, but maybe the shell redirection of the file to stdin interprets the pipe symbol as it would on the command line. If so, escaping it as 2\|7 may work. Or as Teemu suggests, g_select is a more expressive tool once you wrap your brain around it. You should be able to get away with a 2-line script needing no redirection in most (all?) cases. A further clue - groups can be identified by name in GROMACS, so you can make your scripting more meaningful and resilient to change by referring to groups by name rather than number. Next month, you'll have no idea what 2, 7 and 8 are, but their names you'll still understand, hopefully! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv correct the pbc before analysis
On 03/05/12, mu xiaojia muxiaojia2...@gmail.com wrote: Dear gmx users, I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that: use trjconv to account for any periodicity in the system. The protein will diffuse through the unit cell, and may appear to jump across to the other side of the box. To account for such actions, issue the following: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html ) But for my system, I study the short peptides' aggregation, I have many short peptides(not one or two single proteins) and waters, when I use -pbc nojump to treat my trajectory, it only gives me correct short peptides(no across out of the box), but the water is quite diffused. (I guess it is different with the tutorial since on it the protein is 1 or 2 polymers) So (1)how should I analyze such results if I want to study both short peptides(correct coordinates, no crossings) and waters(diffused and crossed box)? That entirely depends on what you are trying to observe. You may find you need multiple representations of the trajectory for different purposes. (2) I tried all the pbc options(even try them one after another, like mol first, nojump second), currently no clues of how to get both peptides and waters correct at the same time. Command for correct protein but incorrect waters' coordinates is: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump Thanks very much, I appreciate any suggestions. If molecules diffuse across the periodic boundaries, you cannot have a single representation that is both compact and lacks jumps. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to extract trajectories into individual pdb file?
On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. See trjconv -h Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv correct the pbc before analysis
On 4/05/2012 4:03 AM, mu xiaojia wrote: Thanks Justin and Mark, I compared g_rama's results for no pbc treated trajectory and pbc treated trajectory, it seems they are the same. So gromacs' analysis tools know how to deal with the broken molecules. Caveat: some tools seem to be better than others at dealing with PBC. There are known question marks hovering over g_dist, g_bond and g_mindist. This situation is probably a consequence of different tools being developed at different times during the evolution of the software suite. Mark But if one want to extract such coordinates out for computing it myself, it is necessary to -pbc mol first, otherwise the molecules might be broken for calculating scripts like matlab. good to know this, thanks! On Wed, May 2, 2012 at 8:03 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 03/05/12, *mu xiaojia *muxiaojia2...@gmail.com mailto:muxiaojia2...@gmail.com wrote: Dear gmx users, I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that: use trjconv to account for any periodicity in the system. The protein will diffuse through the unit cell, and may appear to jump across to the other side of the box. To account for such actions, issue the following: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html ) But for my system, I study the short peptides' aggregation, I have many short peptides(not one or two single proteins) and waters, when I use -pbc nojump to treat my trajectory, it only gives me correct short peptides(no across out of the box), but the water is quite diffused. (I guess it is different with the tutorial since on it the protein is 1 or 2 polymers) So (1)how should I analyze such results if I want to study both short peptides(correct coordinates, no crossings) and waters(diffused and crossed box)? That entirely depends on what you are trying to observe. You may find you need multiple representations of the trajectory for different purposes. (2) I tried all the pbc options(even try them one after another, like mol first, nojump second), currently no clues of how to get both peptides and waters correct at the same time. Command for correct protein but incorrect waters' coordinates is: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump Thanks very much, I appreciate any suggestions. If molecules diffuse across the periodic boundaries, you cannot have a single representation that is both compact and lacks jumps. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Incorrect number of parameters
On 3/05/2012 8:08 PM, Steven Neumann wrote: Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be changed etc. I placed protein-ligan in new box and solvated the system. Now I want to proceed to add ions: grompp -f minim.mdp -c Solv1.gro -p topol1.top -o ions1.tpr Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for LJ-14. Well there is nothing wrong with the topology files as I took them from previus simulation just removing water and ions. I think that Gromacs does not read whole file... Have you ever had such problem? The simplest possible explanation is that your modifications to the .top are not as simple as you believe they are. Check that the original .top works as expected, and use the diff tool to compare the original and modified versions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx angles and dihedrals
On 5/05/2012 1:47 AM, Elton Carvalho wrote: Dear Gromacs users I am currently preparing an RTP file to describe a polymer for use with MARTINI. MARTINI does not include default bonded interactions, so all bonds, angles and dihedrals must be explicitly defined in the topology file or, in my case, in the RTP file. The problem is that pdb2gmx generates at least one dihedral for each bond and an angle for each pair of bonds sharing an atom, even it they are not explicitly defined in the RTP. In that case, pdb2gmx will include the triplet (or quadruplet) for the angle (or dihedral), but with empty parameters, so that grompp looks for general parameters in the forcefield ITP file. With coarse-graned forcefields, it does not necessarily make sense to have all angles and dihedrals, since, for example, rings are modelled as triangles of beads (so that the angles are redundant with the bond lengths) and trans alkyl chains are modelled as colinear beads (such that a dihedral is undefined). Is there a way to prevent pdb2gmx from creating these angles and dihedrals, unless explicity defined in the RTP? Fundamentally, pdb2gmx is built for fine-grained force fields. I'd have supposed Martini has some kind of builder program other than pdb2gmx, for this kind of reason, but I have no idea whether this is true. Setting nrexcl = 1 would exclude such angles and dihedrals, I think, but would also exclude generating the normal ones. One option is to do that and explicitly define the relevant angles and dihedrals. Also, the manual states the following regarding RTP files: The first field in the file is the [ bondedtypes ] field, which is followed by four numbers, indicating the interaction type for bonds, angles, dihedrals, and improper dihedrals. And includes this as an example: [ bondedtypes ] ; mandatory ; bonds angles dihedrals impropers 1 1 1 2 ; mandatory But the aminoacids.rtp file included in the opls-aa forcefield starts with: [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 3 11 3 1 0 Which is inconsistent with the manual. In particular, Col8 set to 1 seems to remove dihedrals over bonds with any dihedral, not only those defined under the [ impropers ] directive. Code comments are in disagreement about column 8. Looking at the code, I think the above .rtp comment is how the code works. A specific simple counter-example (showing how .rtp contents create .itp contents that seem to breach the above description) would be welcome. I'm not sure if there are circumstances where impropers are generated automatically, but that could possibly explain such an observation. Could anyone clarify the role of these extra columns? I think this also hints for a review in this section of the manual. True. An update is in progress now. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Determining which parallelization algorithm I used
On 6/05/2012 7:10 AM, Andrew DeYoung wrote: Hi, I think that Gromacs has two parallelization algorithms as of version 4.5: domain decomposition (the default) and particle decomposition. For my research, I am using the particle decomposition algorithm. Thus, I include the -pd switch when calling mdrun. However, I am worried that in one of my runs I forgot to include the -pd switch. Is there any way to tell from the .log file (or anywhere else in the output) which parallelization algorithm was used. When I search for pd in the .log file, I see several occurrences: --- Division over nodes in atoms: 117311731174117311721175 CPU= 0, lastcg= 1085, targetcg= 3325, myshift=3 CPU= 1, lastcg= 1888, targetcg= 4129, myshift=3 CPU= 2, lastcg= 2690, targetcg= 450, myshift=4 CPU= 3, lastcg= 3494, targetcg= 1254, myshift=4 CPU= 4, lastcg= 4244, targetcg= 2004, myshift=4 CPU= 5, lastcg= 4479, targetcg= 2240, myshift=3 pd-shift = 4, pd-bshift= 0 ... Workload division nnodes: 6 pd-shift:4 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 01173 0 1086 1117311731086 803 2234611741889 802 3352011732691 804 4469311723495 750 5586511754245 235 --- Do the mentions of pd in the above .log file snippets assure me that I indeed used the -pd switch when calling mdrun? Those fragments are indicative of -pd. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Glutamate Chi1 Dihedral Not Symmetrical?
On 6/05/2012 9:27 AM, Sai Kumar Ramadugu wrote: Dear Gromacs Users, I am trying to plot the Ryckaert-Bellemans energy for rotating the chi1 dihedral of glutamate in protein. I tried to change the ch1 dihedral from 0-360 degrees at increments of 1 degree and saved the pdbs. Then I used the pdb's to obtain the corresponding gro files and a single topology file. I used opls force field and no water and a 0 step minimization. If your GROMACS version is up to date, then grompp will have warned you that this is not the best procedure for measuring energies of input configurations. Use mdrun -rerun and a fake trajectory constructed from your sets of coordinates. _My em.mdp file:_ _ _ cpp = /usr/bin/cpp define = -DFLEXIBLE integrator = steep nsteps = 0 constraints = none emtol= 1000.0 emstep = 0.01 nstcomm = 1 ns_type = grid nstlist = 1 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no ;energy groups energygrps = Protein After the minimization, when I plot the dihedral energy vs dihedral angle, I do not get a symmetrical curve. After careful observation of the gro files that I obtained using pdb2gmx, the 0-180 values are not exactly same as -180-0 degrees or 180-360 degrees. Is it because of the slightly different values of the dihedral 0-180 and 180-360 that I'm not getting a symmetrical curve or am I doing something wrong? Only if you vary the dihedral of interest and then follow the above procedure while holding the other internal degrees of freedom fixed will you observe the variation solely due to this RB dihedral. You can plot this more easily from the functional form defined in the force field files, of course. Mark I have attached the dihedral energy vs dihedral angle curve. Regards Sai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?
On 5/05/2012 11:39 PM, Marcelo Lopez wrote: Hi, all, I'm still confused about how to set up 1-4 interaction tables for tabulated non-bonding potentials when using the -tablep option in mdrun. The specific question is: How must I specify the 1-4 interaction in those tables? How many columns and with what? I suggested places to look for this information in answer to this question more than a week ago. http://lists.gromacs.org/pipermail/gmx-users/2012-April/070856.html Your reply addressed only another part of the discussion. Why are you asking the same question again without appearing to have used the help you've been given? My primary goal is to set all the 1-4 interactions equal to zero. I have some 1-4 pairs that aren't involved in dihedrals, that means that setting up nrexcl = 3 and gen-pairs = no isn't enough In what sense? I suggested in that thread that you look at the contents of the .log files to see if any Coulomb 1-4 interactions exist, but you've not replied. Bald assertions that something doesn't work are likely to get people who might help to assume that the most likely explanation is that you're doing something wrong. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem in GROMACS installation
On 6/05/2012 9:08 PM, amit banerjee wrote: Dear Gromacs Users, I am trying to install gromacs 4.5.5 version in a CENTOS 5.4 machine with FFTW 3.3.1. To do so, I have downloaded both the tar.gz files in root and tried to install them as per the standard installation protocol. Unfortunately i am receiving the following error. /usr/bin/ld: /usr/local/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 See http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?
On 7/05/2012 5:50 AM, Marcelo Lopez wrote: For sure, this wouldn't happened if the information to run all the Gromacs features were clearly explained in the place where should be: the manual. Life would be good if everything was perfect, but when you're relying on free software provided by largely volunteer effort, you have to accept some imperfections. Next time save some words and use your time to do a better documentation job... unless you're trying to have some advantage... You started these requests by asserting that no documentation existed. So various people who might have helped you were probably annoyed and decided not to give time to you. However, you got pointed to a likely source of information. You seem to have ignored that. Eventually I got bored of ignoring your repeated requests and pointed you in the right direction again. Others have made worthwhile suggestions, but as far as we know you're ignoring them, too. Your frustration with solving your problem is understandable, but your assumption that you are entitled to perfect free software and to abuse those who help produce it is not understandable. Mark Cheers! 2012/5/5 Mark Abrahammark.abra...@anu.edu.au: On 5/05/2012 11:39 PM, Marcelo Lopez wrote: Hi, all, I'm still confused about how to set up 1-4 interaction tables for tabulated non-bonding potentials when using the -tablep option in mdrun. The specific question is: How must I specify the 1-4 interaction in those tables? How many columns and with what? I suggested places to look for this information in answer to this question more than a week ago. http://lists.gromacs.org/pipermail/gmx-users/2012-April/070856.html Your reply addressed only another part of the discussion. Why are you asking the same question again without appearing to have used the help you've been given? My primary goal is to set all the 1-4 interactions equal to zero. I have some 1-4 pairs that aren't involved in dihedrals, that means that setting up nrexcl = 3 and gen-pairs = no isn't enough In what sense? I suggested in that thread that you look at the contents of the .log files to see if any Coulomb 1-4 interactions exist, but you've not replied. Bald assertions that something doesn't work are likely to get people who might help to assume that the most likely explanation is that you're doing something wrong. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: HEME-cysteine gromacs simulation
Hi, Please send requests for help to the gmx-users mailing list. I (and most others there) are not available as private tutors. Contrary to your assertion below, I've never run any simulations on cytochrome P450. You probably need to name your iron atom more suitably for your force field to recognize (if it can). Mark Original Message Subject:HEME-cysteine gromacs simulation Date: Mon, 07 May 2012 21:04:05 +0800 From: Bing Zhang mpezb...@gmail.com To: mark.abra...@anu.edu.au Dear Mr. Abraham: This is Zhang Bing, from National University of Singapore, writing to bother you for your kind help. I am running into some problems you had a couple years ago when running cytochrom P450 MD simulations: http://lists.gromacs.org/pipermail/gmx-users/2009-August /044495.html . The iron Fe in my cytochrome C is also recognized as Fluorine after run pdb2gmx. I tried so many ways and hope to get the problem solved, unfortunately, failed. I was wondering whether you could kindly give some clues how you solved your problems. I hope the email won't take you too much time, considering it is a quite old question. I have been stuck for a while and my research is now pending here, so any suggestions or advice from you will be greatly greatly appreciated. With best regards, Zhang Bing -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx angles and dihedrals
On 8/05/2012 5:19 AM, Elton Carvalho wrote: Thank you for your reply, Mark, On Sat, May 5, 2012 at 7:06 AM, Mark Abrahammark.abra...@anu.edu.au wrote: Fundamentally, pdb2gmx is built for fine-grained force fields. I'd have supposed Martini has some kind of builder program other than pdb2gmx, for this kind of reason, but I have no idea whether this is true. It kinda does. Not for polymers just yet. I asked part of the people involved in this before asking here. Setting nrexcl = 1 would exclude such angles and dihedrals, I think, but would also exclude generating the normal ones. One option is to do that and explicitly define the relevant angles and dihedrals. nrexcl is already 1, as per MARTINI's defaults and the dihedrals are built anyway. Yeah, I was wrong in that speculation. nrexcl pertains only to non-bonded interactions. Code comments are in disagreement about column 8. Looking at the code, I think the above .rtp comment is how the code works. A specific simple counter-example (showing how .rtp contents create .itp contents that seem to breach the above description) would be welcome. I'm not sure if there are circumstances where impropers are generated automatically, but that could possibly explain such an observation. I prepared a minimal example and, in doing so, I noticed that the problem is not removing dihedrals sharing a bond with impropers, but column 5: all_dihedrals, which is said to generate dihedrals involving ony heavy atoms if set to 0. When set to 1, pdb2gmx generates the dihedrals CA2 CA1 C9 C91 and CA1 C9 C91 C4 for example (see attached figure, remembering this is a coarse grained model), which are not generated when all_dihedrals is zero. Certainly, none of these atoms should be considered light. This raises a question about how heavy atoms are defined in Gromacs. I couldn't find it in the PDF manual. Where should I put the definitions of which atoms are heavy? pdb2gmx looks at whether the atom name starts with 'H' or a digit and then 'H', but it turns out not to be relevant. Also, regardless of the value of RemoveDih, dihedrals like CA2 CA1 C9 C91, that shares the central bond with CA2 CA1 C9 CB1, are kept in the final topology. So apparently RemoveDih doesn't really exclude proper dihedrals sharing the central bond. Yeah, that .rtp comment looks totally wrong. After looking at the code I think: * Column 5: 1 means keep all generated dihedrals, * 0 means permit generated dihedrals to have their parameters * superseded by ones on the same central bond that have * fewer hydrogen atoms. That's totally different from what the .itp suggests, and does explain your observations. There seems to be no automatic way to treat the issue that you'd like addressed. Feel free to make a feature request on redmine.gromacs.org, but it likely won't be addressed until GROMACS 5 (at least). I prepared a minimal structure and a gmxlib tree which includes the RTP file for clarification, but it exceeds the attachment limit of the list, I can send it if its' really necessary Could anyone clarify the role of these extra columns? I think this also hints for a review in this section of the manual. True. An update is in progress now. That's great news! In the next days I'll send some questions about the manual to help guiding that effort! ;) There have been quite a few manual updates already. For example, http://jenkins.gromacs.org/job/Manual_Gerrit_4_5/15/ has a link to a current PDF manual (save as on the PDF link is sometimes necessary). Feedback is welcome, but feedback relative to the updated manual is more welcome. :-) Mark Greetings from a sunny Groningen, -- Elton Carvalho Faculty of mathematics and natural sciences University of Groningen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Treating solute as a rigid body with flexible solvent molecules
On 10/05/2012 7:29 PM, Debayan Chakraborty wrote: Dear Gromacs Users, I want to simulate an organic dye in a solvent ( such as aniline as DMA). I have already relaxed the solvent around the dye in the equilibration run ( NPT) using position restraints on the solute. Now for the production run I want to release the position restraints on the dye and allow it to translate and rotate like a rigid body under the influence of the solvent. I am new to GROMACS, and I am not sure what is the best way to realise this. Any help would be greatly appreciated. This kind of procedure is done in lots of simulations - have a look at some tutorial material and you should learn how to do this, and a lot more besides! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] User defined potential
On 14/05/2012 2:24 PM, mohan maruthi sena wrote: Hi all, I want to define a potential form and give it as input for which i have seen manual ,thought gromacs table option is fine, i have an example of generating 9-6 potential form , My question is how to generate table.xvg, what is the command to generate table.xvg from code table.c. There's no general way to generate new tables from within GROMACS. Some already exist in the $GMXLIB/share folder. mdrun -debug will write out the tables it is using. Otherwise, working out how to take a suitable spreadsheet you have created and export to a text file is often the most straightforward procedure. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun_mpi issue with CHARMM36 FF
On 14/05/2012 3:52 PM, Anirban wrote: Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on more than 5 nodes, the job gets killed with the following error: That's likely going to be an issue with the configuration of your MPI system, or your hardware, or both. Do check your .log file for evidence of unsuitable DD partiion, though the fact of turning on dynamic load balancing suggest DD partitioning worked OK. Mark - starting mdrun 'Protein' 5000 steps, 10.0 ps. NOTE: Turning on dynamic load balancing Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error = = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 256 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES = [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error waiting for event . . . -- Why is this happening? Is it related to DD and PME? How to solve it? Any suggestion is welcome. Sorry for re-posting. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP download,installation and dssp plot
On 14/05/2012 4:14 PM, bunty xy wrote: Hello friends, I am facing problem in using DSSP. I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP Plot ,It generate .dssp file,which have values .But i want the DSSP PLot.Please tell me the installation procedure and download link to get the dssp plot. This forum is for GROMACS-related questions. It is not apparent to me that the plot you seek is GROMACS-related. Perhaps another forum, or the DSSP documentation is what you need. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun_mpi issue with CHARMM36 FF
On 14/05/2012 4:18 PM, Anirban wrote: On Mon, May 14, 2012 at 11:35 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 14/05/2012 3:52 PM, Anirban wrote: Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on more than 5 nodes, the job gets killed with the following error: That's likely going to be an issue with the configuration of your MPI system, or your hardware, or both. Do check your .log file for evidence of unsuitable DD partiion, though the fact of turning on dynamic load balancing suggest DD partitioning worked OK. Mark Hello Mark, Thanks for the reply. The .log file reports no error/warning and ends abruptly with the following last lines: That's most consistent with a problem external to GROMACS. Mark Making 3D domain decomposition grid 4 x 3 x 9, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: Protein_POPC 1: SOL_CL There are: 117548 Atoms Charge group distribution at step 0: 358 353 443 966 1106 746 374 351 352 352 358 454 975 1080 882 381 356 357 357 358 375 770 1101 882 365 359 358 351 348 487 983 1051 912 377 344 361 363 352 596 1051 1036 1050 553 351 349 366 352 375 912 1125 1045 478 351 344 356 362 445 971 1040 959 520 405 355 357 355 639 1032 1072 1096 790 474 353 349 345 449 1019 1047 971 444 354 357 355 357 391 946 1093 904 375 367 368 349 349 409 934 1082 867 406 350 350 364 341 398 978 1104 937 415 341 368 Grid: 6 x 7 x 4 cells Initial temperature: 300.318 K Started mdrun on node 0 Fri May 11 20:43:52 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) U-BProper Dih. Improper Dih. CMAP Dih. LJ-14 8.67972e+046.15820e+041.38445e+03 -1.60452e+03 1.44395e+04 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential -5.21377e+044.98413e+04 -1.21372e+06 -8.94296e+04 -1.14284e+06 Kinetic En. Total EnergyTemperature Pressure (bar) Constr. rmsd 2.93549e+05 -8.49294e+053.00132e+02 -1.80180e+01 1.40708e-05 --- Any suggestion is welcome. Thanks, Anirban - starting mdrun 'Protein' 5000 steps, 10.0 ps. NOTE: Turning on dynamic load balancing Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error = = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 256 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES = [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error waiting for event . . . -- Why is this happening? Is it related to DD and PME? How to solve it? Any suggestion is welcome. Sorry for re-posting. Thanks and regards, Anirban -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support
Re: [gmx-users] line longer than 4095 - a bug?
On 11/05/2012 6:43 PM, Marzinek, Jan wrote: Dear Gmx Users, Many of you probably faced an error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' As I noted this error comes from the changes in the topology. Gromacs somehow add _ and thus this problem occurs. For instance: [ bonds ] ;aiaj functc0c1c2c3 121 131 141 451 461 _ 4241 671 I could not see _ using vi in my topology. However, when I copied all topology to another text editor I could. Then removing it solves the problem. Is that a bug? Don't know - you haven't seen what you were doing when you observed the weird behaviour. So far it sounds like someone has edited a file with an editor that did not save plain text, since 20 is hexadecimal for 32, which is the code for a space character, and maybe some other weird character got rendered with _. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs
On 14/05/2012 6:00 PM, Shima Arasteh wrote: Thanks for your suggestions. Now, I think that it's better to add the N atom of next residue to the .pdb file and then add hydrogen atoms to its .mol2 format. Because when I open formyl.pdb in chimera software and add hydrogens to it, it becomes an formaldehyde and then I get the a wrong parameters in .itp file by using SwissParam. So I didn't remove the N atom which connects to the C of formyl. Now I got this .itp file: ; nr type resnr resid atom cgnr charge mass 1 CR 1 LIG C 1 0.5500 12.0110 2 OR 1 LIG O 2 -0.6800 15.9994 3 HCMM 1 LIG H4 3 0. 1.0079 4 HCMM 1 LIG H6 4 0. 1.0079 5 HOR 1 LIG H8 5 0.4000 1.0079 6 NR 1 LIG N 6 -0.9900 14.0067 7 HNR 1 LIG H2 7 0.3600 1.0079 8 HNR 1 LIG H1 8 0.3600 1.0079 Would this file work probably? I mean can I get the correct parameters? Since you can't have a double bond with that many bonded hydrogen atoms present, no. Like Justin has suggested, one approach is to take the whole residue adjacent to formyl and parameterise all of it. Another would be to take the acetyl group for that force field and assign the total charge of the methyl group to the hydrogen of your formyl - but this has obvious shortcomings. The .rtp file which I arranged, is as below: [ For ] [ atoms ] ; nametype charge chargegroup C CTL1 0.5500 0 O O -0.6800 0 H HC 0.1300 0 [angles ] aiajak O C +N O C H H C +N [ bonds ] C O C +N C H [ dihedrals ] O C +N +CA H C +N +H H C+N+H Would it be correct? I got the charge of H atom by assuming the total charge of formyl is zero. Only if you think the carbonyl group forming an amide bond consists only of atoms with equivalent electronegativity. Any model that does not have partial negative charge on the oxygen will be not worth the time to write down. Mark Sincerely, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sunday, May 13, 2012 9:40 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/13/12 12:42 PM, Shima Arasteh wrote: OK, so I entered the H atom corresponding to the structure and then changed the file as below, [ For ] [ atoms ] ; name type charge charge group C CTL1 0.5700 0 O O -0.5700 0 H HC 0.00 0 I find it highly unlikely that a zero charge should be assigned to this proton. The .itp file you posted before from SwissParam was for formaldehyde, which suggests to me you haven't properly parameterized the species you're looking for and now you're trying to hack something together. Don't try to do that; your parameters will be junk. Parameterize the right species once and proceed from there. [angles ] ai aj ak O C +N O C H [ bonds ] C O C +N C H [ dihedrals ] O C +N +CA H C +N +H There are other possible dihedrals here. -Justin *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Sunday, May 13, 2012 8:36 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/13/12 11:43 AM, Shima Arasteh wrote: Again thanks for all your replies. As I got through your advices, I found that the atoms contribute in making bonds and angles in a residue , or make dihedrals in a residue ( or with atoms in next ones) plus the charge of a the residue should be defined properly in .rtp files to define the new residue in aminoacid.rtp file of CHARMM36 force field. So I arranged this lines to define formyl in .rtp file. And I got the topology. But there are some questions for me here: 1. How can I be sure the formyl which I defined is correct? Is getting the topology is enough to be sure of the correct output? It is incorrect. As I said before, a formyl group is an aldehyde and has an H atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group with an incomplete carbon valence. http://en.wikipedia.org/wiki/Aldehyde The .rtp file for formyl is as below: [ For ] [ atoms ] ; name type charge chargegroup C CTL1 0.5700 0 O O -0.5700 0 [angles ] ai aj ak O C +N [ bonds ] C O C +N [ dihedrals ] O C +N +CA Aside from the missing atom (and resulting missing bonds, angles, and dihedral), the format of this entry is OK. 2. There are lots of numbers in .itp file which I got through the swissparam. But I think the charge of atoms may be
Re: [gmx-users] Virtual Sites - remove from GRO
On 14/05/2012 10:42 PM, Steven Neumann wrote: Dear Gmx Users, i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as VMD write the file using atoms not recognized by pdb2gmx obviously? Please, help! If your original pdb2gmx workflow with virtual sites was recorded in a shell script you'd a) have a record for when you go to write up, and b) be able to do this change easily. As it is, a few minutes with a text editor would probably work for small systems. Alternatively grep -v MCH3 in.gro temp.gro will remove all of the lines for virtual sites named MCH3. Do that for each type of virtual site. Adjust the count of atoms at the top of the .gro file suitably at the end. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT conserved-energy lysozyme
On 15/05/2012 6:17 PM, David de Sancho wrote: Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling thermostat. Check out their paper and see what they claim for conservation properties. In step 6 of the tutorial an NVT equilibration is run using tcoupl = V-rescale. The temperature equilibrates quite rapidly as shown in Justin's webpage. Essentially, T fluctuates around its equilibrium value after ~ 2 ps. However looking at the conserved energy I find that there is a drift that does not seem to plateau even by the end of the 100 ps run (see attachment). Different observables equilibrate over different time scales. I have tried to sort this out myself by using the following settings: (1) change lincs_iter from 1 to 2. (2) change from PME to PME-Switch, which for NVE Gromacs recommends as more accurate (I also modified: rlist=1.0, rcoulomb=1.0, rvdw=1.4). (3) change to vdwtype = Shift, so that errors due to cutoffs were eliminated. None of this seems to help. Actually Justin himself has helped me and found that with the following settings the conservation is considerably better === shift settings === vdwtype = shift coulombtype = PME rlist = 1.4 rcoulomb = 1.4 rvdw = 1.0 rvdw_switch = 0.8 Still there is a drift in the conserved quantity which seems a quite severe problem. Severe sounds like an over-description. The drift is 0.15% in the conserved quantity, beginning from a non-equilibrated starting point and only continuing for about the shortest equilibration period anybody could imagine using these days. There's a lot of approximations going on (PME, rigid bonds, static point charges) and maybe drift at this level is not significant. Still, it should get smaller if you just run for longer. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem in visualizing protein-ion complex trajectory in vmd
On 15/05/2012 10:22 PM, neeru sharma wrote: Dear gromacs users, I am running steered MD simulation using Plumed plugin in gromacs for a system consisting of Protein-Mg-GTP complex. I have to calculate the distance of specific atoms with Mg and GTP. While visualizing the trajectories using vmd, I am encountering some problems. 1) While using the -pbc flag with whole option, the protein is visualized properly, but the Mg and GTP are showing jumps moving away from the protein structure. That is why, the distance between Mg, GTP with atoms of the protein is not coming out properly. 2) While using the -pbc flag with nojump option, the protein is visible in stretched and distorted geometry, but the Mg and GTP are intact with the structure. Here, the distance between Mg,GTP with atoms of the protein is calculated correctly. 3) Then, I tried with both the whole and nojump options,used in succession (first whole and then nojump), but still the protein is not visualized properly. It is visible in stretched geometry only, as was visible with nojump. Can anyone help me regarding the problems I am facing with the visualization? Any help will be highly appreciated. See suggestions here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. You will perhaps need to identify a frame where everything is in the box, and then choose a suitable (new?) group for the various operations, or do multiple passes with trjconv. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Two [ dihedrals ] sections in topology
On 15/05/2012 8:47 PM, Lara Bunte wrote: Hi After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. An an example: First block: [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 119 8 5 6 8 910 5 Second block: [ dihedrals ] ; aiajakal functc0c1c2 c3 1 8 6 4 5180 100 1 2 4 5 5180 100 What could be the reason for this? What do I have to change in my force field folder (CHARMM27) to fix this? Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. In my .rtp file in the force field folder I have only this section for dihedrals [ impropers ] O4 N1 C2 N3 180 100 N1 C2 N3 H3 180 100 This produces your second block of type 5 dihedrals, given what you have said below. I declared my [ bondedtypes ] as the following: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Two [ dihedrals ] sections in topology
On 16/05/2012 4:53 AM, Lara Bunte wrote: Hi Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers. An empty block of dihedrals doesn't hurt, but you don't have one of these. A block of dihedrals lacking parameters gets those parameters looked up from ffbonded.itp. You likely can't have only improper dihedrals and expect any resemblance to the behaviour of the CHARMM27 forcefield. It sounds to me like you're trying to do something that might not be worth attempting, but this thread hasn't revealed your objective. There's no point moving deckchairs on the Titanic if there's icebergs all around. Mark Greetings - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Lara Buntelara.bu...@yahoo.de; Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 17:02 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 5/15/12 10:43 AM, Lara Bunte wrote: Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Normally pdb2gmx will generate proper dihedrals based on bonded connectivity. Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology? What you've been defining as empty is not necessarily so. The fact that parameters are not explicitly printed is not inherently indicative of a problem, since the parameters are looked up from ffbonded.itp and not necessarily recapitulated in the topology. If you get fatal errors about missing parameters, that's a separate issue. [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 force field? Look in charmm27.ff/aminoacids.rtp. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How can i specify a user defined potential between i, i+2 residues
On 16/05/2012 3:43 PM, mohan maruthi sena wrote: Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Doing that with a user-defined non-bonded potential requires you change nrexcl for your force field. Doing that with a user-defined bonded potential doesn't, but you'll have to specify all the interactions manually. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.
On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs http://lammps.sandia.gov/ and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs http://lammps.sandia.gov/. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Various files in src/mdlib/ deal with these kinds of algorithms. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nvt equilibration output
On 16/05/2012 4:18 PM, priya thiyagarajan wrote: Respected sir, I am studying about micelle formation .. After setting box and adding water i went for energy minimization and then went for nvt equilibration for 1ns. when i visualized my nvt.pdb file, i found that my protein comes together and formed three micelle like structure. but my box got separated. i dono why i got two separate box. can anyone tell me why this occurs.. i tried many times.. but still i am getting the same.. but i already performed dynamics for 30 monomers.. that time it went well.. now i am getting my output like this.. i checked the system temperature.. its in equilibrium at 299.9k. Whatever you're observing is almost certainly normal, and you need to be sure you understand http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. The advice there, and perhaps further options you can see in trjconv -h will be necessary to manipulate the trajectory so that it looks the way you want it to. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: NVT conserved-energy lysozyme
On 16/05/2012 1:50 AM, daviddesancho wrote: Thanks Florian and Mark for your replies. I have run the simulation for longer (one order of magnitude longer, i.e. 1 ns) and what I get now is that the 'conserved energy' follows its drift linearly. Now, of course, we are speaking about 1.2% drift/ns in the value of the energy, which seems quite substantial. http://gromacs.5086.n6.nabble.com/file/n4981453/equil_nvt.png Second, I have compiled and run with double precision. Although the value for the conserved energy is slightly different, the slope of E vs time is essentially identical. -- View this message in context: http://gromacs.5086.n6.nabble.com/NVT-conserved-energy-lysozyme-tp4980918p4981453.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. What's your full .mdp and GROMACS version? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP configuration in Gromacs 4.5.5
On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP configuration in Gromacs 4.5.5
On 16/05/2012 5:33 PM, Sathish wrote: Dear Sir, Thank u for reply and the old dssp executable was working fine, [root@localhost]# dssp COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by elmar.krie...@cmbi.ru.nl mailto:elmar.krie...@cmbi.ru.nl / April 1, 2010 USAGE dssp [Options] PDB_File DSSP_File - Read PDB_File and write DSSP_File dssp [Options] -- dssp_file - Read from stdin and write DSSP_File dssp -h - Display this help screen OPTIONS -na Disables the calculation of accessible surface. -cClassic (old) format. -wWide 2002 format (for future use,not the current standard). -vVerbose. --Read from standard input. -h -? Prints a help message. -VPrints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By emmanuel.cource...@toulouse.inra.fr mailto:emmanuel.cource...@toulouse.inra.fr -ssa Adds information about disulfide bonds to output file -xRenames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends [root@localhost]# and i have checked one again the path of DSSP [root@localhost sathish]# echo $DSSP /usr/local/bin/dssp [root@localhost sathish]# but while running with do_dssp has problem. [root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5-dev-20120318-375fa98 (-: You are not using 4.5.5. If you'd shown this the first time, you'd have used less of everybody's time. Maybe this version is one that is updated to use the new DSSP. Maybe you should go and use 4.5.5. Also, don't do routine work logged in as root, unless you like reinstalling your whole operating system. Mark . . . Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Segmentation fault (core dumped) [root@localhost sathish]# Am not clear to understand this problem. help me -- -- Regards, N. Sathishkumar, mailto:sath...@khu.ac.kr On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx Warning: Long Bond
On 16/05/2012 5:50 PM, Lara Bunte wrote: Hi If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got warnings like this: Making bonds... Warning: Long Bond (1-2 = 0.261872 nm) Warning: Long Bond (2-4 = 0.267812 nm) Warning: Long Bond (6-4 = 0.260531 nm) and so on For what problem tries GROMACS to warn me? Should I change something? That depends whether your molecule should have bonds this long in the configuration you provided to pdb2gmx... but since you've kept the nature of your molecule a mystery, you'll have to answer that yourself :-) In my .rtp parametrization file in the CHARMM27 folder I gave the equilibrium bond length in angstrom with corresponding force constant in kcal/mol, that are out of a supporting Information of a group, that made quantum mechanical calculations with my molecule. See chapter 2 for the acceptable gromacs units. These do not include Angstrom or kcal/mol. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] charm in gromacs
On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had no reason to upgrade these conversion scripts to support function type 9. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.
On 17/05/2012 11:48 AM, kevin wrote: Thanks. I think I should have a look at some specific documents to understand the flow of control. Namely, to understand what is purpose of the subroutines in src/mdlib/. But I could not find such information in the Gromacs user manual. Do anyone know such an document? Thanks. Unfortunately the development of GROMACS is not fast enough to suit anybody's wishes, and too fast and complex to make it worth people's volunteer time to do much beyond what can be observed by inspecting the code. I suggest you step through a run of GROMACS with your favourite debugger on a similar calculation and observe the control flow. There is some discussion of data structures on the GROMACS webpage which is more-or-less useful for the 4.0/4.5 series. Mark kevin.len *From:* Mark Abraham mailto:mark.abra...@anu.edu.au *Date:* 2012-05-16 13:57 *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org *Subject:* Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks. On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs http://lammps.sandia.gov/ and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs http://lammps.sandia.gov/. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Various files in src/mdlib/ deal with these kinds of algorithms. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp error - incorrect number of parameters
On 17/05/2012 11:47 PM, Lara Bunte wrote: Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology I have function 4 (for improper dihedrals): Out of topol.top [ dihedrals ] ; aiajakal functc0c1c2 c3 1 8 6 4 4180 100 And in my .rtp file in the CHARMM27 force field folder I have: Out of .rtp file ; bonds angles dihedrals impropers 1 5 44 There's no aminoacids.rtp file for CHARMM27 that has ever looked like this. Any that did is not CHARMM27. Mark and in my ffbonded.itp file I have: [ dihedraltypes ] ; i j k l funcq0 cq ON1 NN3A CN1A NN2U 4 180 100 So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization file I have the function 4 for the improper dihedrals. What is the problem? Thanks for helping me Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors.
On 18/05/2012 4:43 PM, Seera Suryanarayana wrote: Dear all, While i am running gromacs software i am getting following error.Let me know how to over come that error Fatal error: number of coordinates in coordinate file (208L_ion.gro, 62283) does not match topology (208L.top, 62293) The number of coordinates must match. See discussion of the [molecules] section in chapter 5 of the manual. That's probably what you should fix, probably with the number of solvent and ion atoms changing. genion -p will do this for you if you tell it to do so. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding error.
On 18/05/2012 4:50 PM, Seera Suryanarayana wrote: Dear all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Residue 'CSD' not found in residue topology database Please search for your own answers before posting. You'll learn more and faster! This error, and most others, are discussed here: http://www.gromacs.org/Documentation/Errors Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] repulsive interaction i and i+2
On 18/05/2012 6:14 AM, mohan maruthi sena wrote: Hi all, I have used a user define potential to describe attractive potential beyond i and i+3 atoms(similar to lLJ). If i want to describe repulsive interactions with in i and i+3 , how can i do it in gromacs? can anyone suggest me a way, You can have multiple user-defined potentials if you can set up energy groups within which they interact, but I don't think it is possible in the current code to have the potential vary with the bonded connectivity. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] restart REMD
On 23/05/2012 1:24 AM, Tomek Wlodarski wrote:
Hi,
-s before -deffnm works, now after starting once more REMD from
the scratch I can do restart.
I use
mpirun mdrun_mpi -multi $nrepls -deffnm ${name}_sim $npme -cpi
${name}_sim -append
and it Just Works with 4.5.5.
Mark
Thanks.
Best
tomek
On Mon, May 21, 2012 at 2:39 AM, mu xiaojia muxiaojia2...@gmail.com
mailto:muxiaojia2...@gmail.com wrote:
try put -s before -deffnm
mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append
On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski
tomek.wlodar...@gmail.com mailto:tomek.wlodar...@gmail.com wrote:
Hi Francesco,
Thanks!
However, it does not work with my case..
tomek
On Sun, May 20, 2012 at 1:47 PM, francesco oteri
francesco.ot...@gmail.com mailto:francesco.ot...@gmail.com
wrote:
Hi,
usually I use something like:
mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt*
*
*
gromacs is smart enough to understand that it has to load
topol_1.cpt topol_2.cpt ecc.ecc
Anyway, you can do a small test, i.e. using 5 replicas and
stopping you simulation after a few seconds
Francesco
2012/5/20 Tomek Wlodarski tomek.wlodar...@gmail.com
mailto:tomek.wlodar...@gmail.com
Hi,
I am running REMD simulation:
mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000
I am getting files with name like -s* (for example
-s1.trr)
How now I could restart this simulation?
I know that for regular MD simulation only I need -cpi
cpt_file_name --append to add, but what with REMD
simulation (I have cpt file: for example -s1_prev.cpt?)
Something like: -cpi -s ??
Thanks for suggestions!
Best!
tomek
--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
Please don't post (un)subscribe requests to the list.
Use the
www interface or send it to
gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
Cordiali saluti, Dr.Oteri Francesco
--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: LIE methodology check
On 23/05/2012 8:36 AM, Tom Dupree wrote: Greetings all, I now realise I asked too many questions with that one post. I would like to check that mdrun -rerun can be used to do single point energy calculations on the co-ordinate frames from my trajectory using a different electrostatic model by changing the .mdp file used by grompp to build the .tpr file? Yes. You can observe differences from your original run, even with identical .tpr and thus model, because the rerun does (for example) neighbour searching for every frame, since it cannot assume atoms in nearby frames share spatial locality. Obviously there is no way to know if that frame would be present in the ensemble produced by the new .tpr, but you can measure the energy if you want to. Mark All the best, Tom ___ Message: 2 Date: Mon, 21 May 2012 03:26:07 + From: Tom Dupreet.dup...@unsw.edu.au Subject: [gmx-users] LIE methodology check (mdrun -rerun cutoffs and box vectors) To: gmx-users@gromacs.orggmx-users@gromacs.org Message-ID: 0a0e67195a48dc4a96321968e2b384b024bf6...@infpwxm007.ad.unsw.edu.au Content-Type: text/plain; charset=windows-1252 Greetings all, Background: I have a series of MD runs of a protein ligand complex where I have used PME, they represent far more calculations than I have time to repeat in full. I recently became aware that the coulombic interaction energy reported when PME is used is not valid for use with g_lie (or any LIE method). I have read some relevant LIE papers and it seems that reaction field is the electrostatic method used. http://pubs.acs.org/doi/abs/10.1021/jm7012198 Current methodology: I found that using mdrun ?rerun and a new .tpr file I can change reported energies. Are these energies corresponding to the settings in the new .mdp file? Can I change it from PME to Generalised-Reaction-Field? Are there any errors associated with changing it, as opposed to errors implicit in either method? I am understanding ?rerun to only be calculated for the co-ordinate frames that are outputted into the .xtc file irrespective of any settings in the new .mdp file and/or old .mdp file for the energy. As I only outputted .xtc files I don?t have velocities (or did I set that in the .mdp file?) but I assume that errors in kinetic energy, temperature and pressure are not important in the rerun as I am only concerned with interaction energy? Right assuming all the above is valid I would like to improve my accuracy as much as possible. My understanding of cut offs is that the bigger they are the more accurate and the more computationally expensive your calculations are until they approach half the shortest box vector where pbc issues cause errors. As I am only doing reruns now I should use the largest possible cut offs that don?t hit the pbc limit? Is there an accuracy difference between the short range and long range calculations for the LJ potential? (is there a reason to use long range at all?) For the reruns can I ignore the problem of a water molecule seeing both sides of my protein and use a cut off greater than the editconf -d setting (in my case 1.6)? Or to be strictly accurate should I work out the distance to the other side of the mirror protein from the binding site via the pbc boundary and use half that? Which brings me to my issue with the unit cell. I set -bt dodecahedron. But I don't see it as one (vmd/pymol display of water atoms/unit cell). How do I relate the vectors in the.gro file to the pbc arrangement? 2584CL CL 7792 5.230 2.213 3.017 0.0075 0.3566 0.5809 2585CL CL 7793 1.448 2.710 1.489 0.5771 0.2054 0.0146 2586CL CL 7794 3.070 1.270 3.024 -0.1756 -0.0490 -0.1351 2587CL CL 7795 5.112 2.558 1.562 -0.1543 -0.0592 -0.0072 2588CL CL 7796 2.906 1.133 1.094 -0.2265 -0.3952 0.1190 4.80953 4.80953 3.40085 0.0 0.0 0.0 0.0 2.40476 2.40476 -- In my trials I got the error ?ERROR 1 [file topol.top, line 50]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist.? So if I understand the .gro file correctly (now) these vectors are the long diagonals of three rhombuses. Two are at right angles to each other and the third connects two a lower edge on each of those. Trial and error lead me to the maximum cut off that grompp will accept is 2.40476, which is d/2, if I read this correctly. My question is, why don't my waters and/or unit cell appear to be a dodecahedron when viewed in VMD/pymol? For that matter why don't the waters and unit cell agree on a shape when viewed in VMD? (both are rhombic prisims). All the best, Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] gromacs input file
On 23/05/2012 4:20 AM, Muyi Xu wrote: Hello I am trying to change a crystal structure(wih amc or cif format) into a .pdb format; but gromacs gives me input/output error; which means my input file has the wrong format. Do u have any suggestions how to convert or what software to use? Perhaps you can go back to the original source and get a .pdb file, or ask Google for options. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top/itp file to show parameters explicitly
On 23/05/2012 6:42 PM, Alan wrote: Thanks Justin, you were right. In the end gmxdump helped to clear some doubts but I wished it would be less painfully. One useful approach is to simplify the system as much as possible before producing the .tpr and using gmxdump. The necessary cross-referencing is easier to see when the complexity of the contents is low. Mark Cheers, Alan On 22 May 2012 12:36, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/22/12 12:46 PM, Alan wrote: Hi Justin, your suggestion got close. However, let me give an example. You can use the Gly-Gly-Gly example I am attaching and do this: pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none /sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp aGGGp.top if you look at aGGGp.top I can't find which parameters were used for [ dihedrals ] ; aiajakal functc0c1 c2 c3c4c5 2 1 5 6 9 I.e., for proper dihedral (H1- N-CA- HA1), I can't find in amber99sb.ff/forcefield.itp any combination that handles parameters for X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral? Make sure you're looking at types, not names. The type sequence here is H-N3-CT-HP, which I think is mapped to this dihedral: X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230 Running gmxdump on the .tpr file will show it for sure; I had assumed it would be in the post-processed topology as well, but I guess not. -Justin Thanks, Alan On 21 May 2012 18:50, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/21/12 2:43 PM, Alan wrote: Hi there, Is there an option in pdb2gmx that when generating the top/itp file, it could show the parameters explicitly? e.g.: Instead of: [ dihedrals ] ; aiajakal functc0 c1c2 c3 5131112 4 11151314 4 15232122 4 21252324 4 25323133 4 (my hard hand modifications) [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i j k l func phase kd pn 5 13 11 12 4 180.00 43.93200 2 ; CA- N- C- O 11 15 13 14 4 180.00 4.60240 2 ; C-CA- N- H 15 23 21 22 4 180.00 43.93200 2 ; CA- N- C- O 21 25 23 24 4 180.00 4.60240 2 ; C-CA- N- H 25 32 31 33 4 180.00 43.93200 2 ; CA- OC1- C- OC2 I mean, if the parameters that are hiding in e.g. ...gromacs/top/amber99sb.ff could be showed in the top/itp file for human readers, that would be great. You can obtain these parameters (I believe) by running grompp with the -pp option. If you think it would be a useful feature for pdb2gmx, file a feature request on redmine.gromacs.org http://redmine.gromacs.org http://redmine.gromacs.org. -Justin -- ==__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] electrostatic component of the forces
On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote: Hi all, I am trying to get the electrostatic forces acting on each atom as a function of time. I have checked the list and all the suggestions are based on rerunning the simulation. Is there not an easy way to print these forces on the fly ? You can print the whole force on the fly with nstfout, but you cannot decompose it. If not, what is the cleanest way to remove bonded and vdw components from the forces ? One option could be to set all the unwanted interaction to zero in the topology file but I am wondering if there is a safer alternative. The code permits such a safe alternative, by not setting GMX_FORCE_BONDED, but there is no way to access that setting from the command line. The best you can easily do is mdrun -rerun with parameters zeroed. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unknown cmap torsion between atoms
On 25/05/2012 7:52 PM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes). Then when I process to grompp the error: unknown cmap torsion between atoms ... These atoms belong to the last residue of the chain A and to the first residue of Chain B. How to get rid of this? Please, help. What version is this? I seem to recall fixing this bug at some stage. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] xtc-precision
On 28/05/2012 7:48 AM, Justin A. Lemkul wrote: On 5/27/12 5:29 PM, Igor Druz wrote: I would like to save disk space and write only protein coordinates using xtc-grps, but preserve the same precision as in trr file. What value of xtc-precision should be used to achieve this? Why not write a .trr file with the desired frequency? What you're looking to do is no different than setting a non-zero value of nstxout, with nstfout and nstvout set to zero. You need to choose a large .xtc precision, or use nstxout and filter the group afterwards. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] xtc-precision
On 28/05/2012 8:14 AM, Igor Druz wrote: / You need to choose a large .xtc precision, or use nstxout and filter the group // afterwards./ / / /I tried xtc-precision=100. This gives the same result as the default value//xtc-precision=1000./ That seems highly unlikely. Can you demonstrate that with gmxdump of the two files? / Yet, the results are different from the analysis of the trr file./ Necessarily. Of course, there may not be any value in saving the coordinates in high precision. The errors from incomplete sampling and an approximate model physics will dominate at some point. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS Installation problem: libfftw3f.so.3: cannot open shared object file
On 29/05/2012 3:09 PM, a a wrote: Dear Sir/Madam, Follow the steps below, I have installed fftw library and gromacs as a root. (1) tar -xzvf fftw-3.0.1.tar.gz (2) cd fftw-3.0.1 (3) ./configure --enable-float --enable-threads --enable-shared Here you enabled threads for fftw, which is not recommended here http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite. I don't know whether that's a problem, but certainly it will not help. (4) make (5) make install (6) tar -xzvf gromacs-4.5.5.tar.gz (7) cd gromacs-4.5.5 (8) ./configure (9) make (10) make install (11) I have also add PATH=/usr/local/gromacs:$PATH; export PATH to my .bashrc file in my directory. See http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation for the recommended procedure. However, I have problem to do the following comments: /usr/local/gromacs/bin/g_covar -s test.pdb -f test.netcdf -o -v /div The follow error message appears: /usr/local/gromacs/bin/g_covar: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such file or directory I found the following libraries in my /usr/local/lib directory: libfftw3f.a libfftw3f.so.3.0.1libfftw3f_threads.so.3 libfftw3f.lalibfftw3f_threads.a libfftw3f_threads.so.3.0.1 libfftw3f.solibfftw3f_threads.la pkgconfig libfftw3f.so.3 libfftw3f_threads.so Thus, it seems to me that libfftw3f.so.3 is already installed, whats' wrong with this? Could you mind to help. Your system apparently doesn't have this location in the search path for shared libraries. Maybe following http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation will fix that. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Measure of density in homo- and heterogeneous systems
On 29/05/2012 3:21 PM, James Starlight wrote: Justin, the main problem is the my simulation in nvt ensemble :) I understand that density is constant in that conditions but I'd like to find way to check this values for different components of my system. AFAIK, there's no easy way to do that with GROMACS tools. The problem lies in defining the shape over which you want to compute such a partial density, since you need to compute its volume. Any solution is likely to be at least a bit crude, even for a trivial case of a membrane-mimic in water whose interfaces are roughly orthogonal to a box vector. g_select may be useful in forming a suitable subset, and g_sas may be suitable for computing density and/or volume. Mark James 2012/5/28 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 5/28/12 3:09 PM, James Starlight wrote: Dear Gromacs users! In this task I have two systems: First system consist of single layer of Ccl4 molecules. Second system consist of membrane-mimicking layer of Ccl4 surrounded by water and the protein embedded in that biphastic layer. I'd like to measure density in both of my systems to check of its packing degree. How could I do it in the case of homo system- (where I'd like to check density in the Ccl4 layer only) as well as in more complex hetero system ( where I'd like to check density in each layer separately as well as compute averaged density among all layers) ? The density of the homogeneous system can easily be obtained from the .edr file, as long as the ensemble was NPT. With NVT, the density term is not written, IIRC. In the case of the heterogeneous system, use g_density to obtain partial densities as a function of box dimension. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating number density using g_density
On 27/05/2012 2:00 AM, Andrew DeYoung wrote: Hi, It is possible to compute the number density using g_density, with the switch -dens number. Do you know if this is the number density of molecules? Or is it the number density of atoms? I'd expect atoms, but you should be able to test for this easily. Ideally, I would like to compute the number density of _molecules_. Specifically, I would like to use the center of mass of each molecule to represent that molecule's position. Then the center of mass of each molecule should be used to calculate the number density of molecules. Do you know if this is possible using any of the Gromacs utilities? Not natively. g_traj -com can compute centers of mass of groups, which you could assemble into a pseudo-trajectory using a script you wrote yourself. g_density -dens number should then work on molecules as you intend. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] charm in gromacs
On 18/05/2012 8:02 PM, francesco oteri wrote: Hi, at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can find the files I am using Files ffcharmmnb.itp ffcharmmbon.itp have been generated through: convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl/ par_all36_carb.prm while carbohydrates.rtp and carbohydrates.rtp through a script of mine. Now, if you look at [ dihedraltypes ] section in file ffcharmmbon.itp, there are strange things: 1) dihedrals defined once, are converted Ryckaert-Bellemans form, while the armonic form should be more clear. Anyway, it just a matter of style so I dont complan about. 2) dihedrals with multiple definitions ( OC30P CC3162 CC3161 OC311 at line 598 in file ffcharmmbon.itp, for example) are defined as: OC30P CC3162 CC3161 OC311 3 20.92 41.84 16.74 -41.84 0 0 ; 30P CC3162 CC3161 OC311 1 180 10.46 1 ; 30P CC3162 CC3161 OC311 1 0 8.368 2 ; 30P CC3162 CC3161 OC311 1 0 10.46 3 The commented lines clearly display the multiple definition, that can be described using function 9 ... which didn't exist at the time of my writing of that script, as the comments in the script discuss. Hence solution 1), which was adequate for the subset of CHARMM27 that was of interest to me. 3) An other problem rise with impropers dihedrals. Any of them are defined as Ryckaert-Bellemans, ex. HCA1 CC3161 CC3162 OC311 3 0.5858 1.757 0 -2.343 0 0 at line 926 of ffcharmmbon.itp while points 1 and 2 don't impact on the correctness of the simulation and can be bypassed defining [ bondedtypes ] section as following 1 5 321 3 1 0 Problem 3 cannot be solved without manipulating the ffcharmmbon.itp. In fact, since some impropers are defined as functiontype 2 other as functiontype 3, so there is not an unique bondedtypes definition covering both the definition. Did I any mistake or actually there is a problem in the script? IIRC CHARMM36 is more recent than that script, so the assumptions made by the script for CHARMM27 may not be applicable. If CHARMM36 uses more than one kind of improper dihedral, then I would not expect the script to function correctly in this regard. You would need to modify the script or its output. Mark Francesco 2012/5/18 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had no reason to upgrade these conversion scripts to support function type 9. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to install GROMACS in 64-bit?
On 29/05/2012 6:37 PM, a a wrote: Dear Sir/Madam, Thanks for the insightful comments from the experts.Follows the steps, I found the source of error: This what I have done: In the following directory /home/softwares/fftw-3.0.1: ./configure --enable-shared --prefix=/home/softwares/fftw301 make make install In the .bash file: export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib go to the following directory /home/softwares/gromacs-4.5.5: ./configure --enable-shared --prefix=/home/softwares/g455 make = == In the middle of the make, I found this error message: == /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit machine and the OS is also 64 bit, what should I do to make sure both the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings? I would start by observing that those error messages pertain to an installation of FFTW that configure found in /usr/local/lib, and not the one in /home/softwares. You have to sort that out first, since this error messages indicates the need to use FFTW configured with --enable-shared, per the link I gave last time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to install GROMACS in 64-bit?
On 30/05/2012 1:50 AM, a a wrote: Dear Mark, I have overlook it. Sorry. I have already added the following two sentences in .bashrc file in my home directory (when I login as user). export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib Should I type in another lines? They won't help until you start a new shell. Or, instead, use them on the command line like the installation instructions suggest - since you don't need these settings on an ongoing basis. Did I do any common mistakes in using the command export with .bash shell? Should I add these two lines at the root directory as it seems I have a role as root during installation? Definitely not. make install is the only command for which you should be root, and only then if the installation location requires it. Unless you like pain from risking needing to reinstall your trashed system. Mark Please kindly give me some more guidance. Many thanks, Catherine Date: Tue, 29 May 2012 18:48:15 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] How to install GROMACS in 64-bit? On 29/05/2012 6:37 PM, a a wrote: Dear Sir/Madam, Thanks for the insightful comments from the experts.Follows the steps, I found the source of error: This what I have done: In the following directory /home/softwares/fftw-3.0.1: ./configure --enable-shared --prefix=/home/softwares/fftw301 make make install In the .bash file: export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib go to the following directory /home/softwares/gromacs-4.5.5: ./configure --enable-shared --prefix=/home/softwares/g455 make = == In the middle of the make, I found this error message: == /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit machine and the OS is also 64 bit, what should I do to make sure both the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings? I would start by observing that those error messages pertain to an installation of FFTW that configure found in /usr/local/lib, and not the one in /home/softwares. You have to sort that out first, since this error messages indicates the need to use FFTW configured with --enable-shared, per the link I gave last time. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trajectory analysis
On 30/05/2012 4:45 PM, oguz gurbulak wrote: Dear All, I want to ask some questions about trajectory analysis. I have some md simulation output files that includes coordinate, force and velocity information. And these files are huge ( more than 5 GB ) . Could you please recommend a free text editor which works on Linux or Windows to open and editthese huge files? And I will run these files with fortran codes and get again huge output files . In order to do this operation faster and seamlessly what should I do ? Which facilities do I have on pc ? Could you please share your experiences with me ? The advice of http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume is applicable to managing these situations. A few minutes of thought can save hours of I/O processing. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions
On 30/05/2012 5:33 PM, MD wrote: Hi All, I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. By finding the method that was used then and attempting to replicate it? Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated, A certain degree of pickiness is essential. You're apparently trying to replicate a result by making some arbitrary choices. Don't. This .mdp file generates velocities, thus did not start in an equilibrium ensemble. However you measured your surface tension needs to exclude the equilibration time. Mark The main parameter is coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 The full .mdp are as follow, ; ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: chagall ; At date: Mon Dec 15 13:13:06 2003 ; ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 40 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size ; Max number of iterations in relax_shells niter = 20 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5000 nstvout = 8000 nstfout = 8000 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 5000 ; Output frequency and precision for xtc file nstxtcout = 500 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing
Re: [gmx-users] Fw:Re:gmx-users Digest, Vol 97, Issue 218
On 30/05/2012 7:24 PM, MD wrote: Yes, i try to get a surface tension of 69 dyn, but i can only get 65 at present. Yes, i tried some arbitrary choices. I do not know what is the correct .mdp for me to get a surface tension of 69. May be for this version, it does not include this function Making arbitrary choices is a bad approach. When that fails, assuming that there's a limitation in the software that you are using is even worse. Someone used a specific method to get the number someone claims you should be getting. You need to go and find out what that that method was. Yes, this is more work than assuming that GROMACS can't reproduce the method. Welcome to the jungle :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] angling bond at at one of the terminal ends
On 30/05/2012 9:30 PM, ramaraju801 wrote: hi, recently while working on gromacs i came across this error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried to edit .tdb file by giving the terminal entries but its not working.. plz help me out You need to describe what you are trying to do and how you attempted to do it in a lot more detail before anybody can help you. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Possible bug: energy changes with the number of nodes for energy minimization
On 30/05/2012 9:42 PM, Stephen Cox wrote: Hi Justin, Thanks for getting back and posting the links. On 5/29/12 6:22 AM, Stephen Cox wrote: Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are: #cores energy 1-2.41936409202696e+04 2-2.43726425776809e+04 3-2.45516442350804e+04 4-2.47003944216983e+04 #threadsenergy 1-2.41936409202696e+04 2-2.43726425776792e+04 3-2.45516442350804e+04 4-2.47306458924815e+04 I'd expect some numerical noise, but these differences seem to0 large for that. The difference is only 2%, which by MD standards, is quite good, I'd say ;) Consider the discussion here: I agree for MD this wouldn't be too bad, but I'd expect energy minimization to get very close to the same local minimum from a given starting configuration. The thing is I want to compute a binding curve for my clathrate and compare to DFT values for the binding energy (amongst other things), and the difference in energy between different number of cores is rather significant for this purpose. Given the usual roughness of the PE surface to which you are minimizing, some variation in end point is expected. Furthermore, if I only calculate the energy for nsteps = 0 (i.e. a single point energy for identical structures) I get the same trend as above (both mpi/openmp with domain/particle decomposition). Surely there shouldn't be such a large difference in energy for a single point calculation? nsteps = 0 is not strictly a single-point energy, since the constraints act before EM step 0. mdrun -s -rerun will give a single point. This probably won't change your observations. You should also be sure you're making observations with the latest release (4.5.5). If you can continue to observe this trend for more processors (overallocating?), then you may have evidence of a problem - but a full system description and an .mdp file will be in order also. Mark http://www.gromacs.org/Documentation/Terminology/Reproducibility To an extent, the information here may also be relevant: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation Before submitting a bug report, I'd like to check: a) if someone has seen something similar; Sure. Energies can be different due to a whole host of factors (discussed above), and MPI only complicates matters. b) should I just trust the serial version? Maybe, but I don't know that there's evidence to say that any of the above tests are more or less accurate than the others. What happens if you run with mdrun -reprod on all your tests? Running with -reprod produces the same trend as above. If it was numerical noise, I would have thought that the numbers would fluctuate around some average value, not follow a definite trend where the energy decreases with the number of cores/threads... c) have I simply done something stupid (grompp.mdp appended below); Nope, looks fine. -Justin Thanks again for getting back to me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond
On 31/05/2012 4:42 PM, Acoot Brett wrote: Dear All, The value of the energy of the hydrogen bond has relation with distance and angle of the hydrogen bond related atoms. As for in the simulation process, the distance and angle of the hydrogen bond related atoms may change continuously. Will you please let me know based on which formula GROMACS calculated the value of the energy of the hydrogen bonds? There is no such formula used in MD force fields implemented in GROMACS. The only non-bonded interactions are the ones you already know about: electrostatics and VDW. Observables like hydrogen bonds and the hydrophobic effect arise from them. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.
On 31/05/2012 4:13 PM, ramaraju801 wrote: when i ran gromacs to produce topology file for a nucleotide sequence it is showing the above error saying There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. ... or maybe you need to use pdb2gmx correctly. Since you haven't told us how you've used it, we can't help. Make sure you've done any DNA-protein tutorials you can find, and applied any lessons you may learn. i tried giving the starting and ending residues in .n.tdb and .c.tdb files but it did not work with an error saying Fatal error: reading termini database: directive expected before line: P So you've broken the file format. Re-read the relevant part of chapter 5 of the manual and try again. Mark am uploading my PDB file of my DNA-protein compex sequence in which the nucleotide sequence ranges from 1 to 12216 http://gromacs.5086.n6.nabble.com/file/n4997922/dnaseq_rot1.pdb dnaseq_rot1.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/dangling-bond-at-at-least-one-of-the-terminal-ends-and-the-force-field-does-not-provide-terminal-ent-tp4997922.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating the average separation between two multi-atom groups
On 31/05/2012 11:24 AM, Andrew DeYoung wrote:
Hi,
I have a system in a slab geometry. A surface exists at z = 0; many
hydrogens protrude from the surface, and these hydrogens are mostly (but not
precisely) immobile. Above the surface, there is liquid, including the
anion BF4- (tetrahedral arrangement of fluorines around a central boron).
The liquid region is large, extending far from the surface, (far above the
surface, the liquid behaves like liquid in the bulk).
There is hydrogen-like bonding between the hydrogens protruding from the
surface and the fluorines in BF4-. I would like to calculate the average
H-F distance, where H atoms protrude from the stationary surface and F atoms
exist on the BF4- ions. But saying that I want to compute the average H-F
distance is very vague. I can think of at least two possible, hopefully
reasonable, ways to formulate the problem:
(i) For the purpose of calculating the average H-F separation, only consider
fluorines on BF4- ions which are within a certain perpendicular distance z0
from the surface. In other words, consider the BF4- ions which lie in the
region 0 z z0 (where z0 is positive and very small compared to the z
dimension of the simulation box). Then, using those BF4- ions, I calculate
the (time-averaged) H-F separation.
(ii) For the purpose of calculating the average H-F separation, only
consider fluorines when they are a certain small distance from any hydrogen.
Are (i) or (ii) these feasible?
For (i), I can think about using g_select to select BF4- ions which are a
distance of z0 or less from the surface at z = 0. Maybe I would use a
selection like 'res_com of resname BF4 and z 10' (where z0 = 10). The
problem with this is that, I think, I would obtain an index file for each
simulation timestep.
Yes, you'd need to do some iteration over g_select and then another
tool. GROMACS 5 will likely do that for you, but nirvana is some way off...
So, I guess then if I have 200,000 simulation
timesteps, I would have to run g_bond 200,000 times! (Or would g_dist be
appropriate here?) Also, even my formulation in (i) is a little awkward;
fluorines at one edge of the xy dimension would be far from hydrogens
immobilized at the other side of the xy dimension, so I would get artifacts.
These tools *should* work correctly with PBC, but I would advise
checking that they do, e.g. by making some very small subsets that you
know cross boundaries and checking their stats agree with subsets that
you know do not cross boundaries.
For (ii), it seems that g_hbond might be useful. However, it does not seem
that fluorine is currently implemented as a hydrogen bond acceptor for use
in g_hbond. I have never attempted to modify the Gromacs code and I am not
sure how easy this would be. But if H-F is a hydrogen-like bond, then
(average) H-F bond length is what I am going after, I guess.
Do you know of any recipes with which to do this, or do you have any
suggestions? Thanks so much!
You can match the trajectory to some .tpr that didn't create it. So if
you generate a new topology that uses PO4 instead of BF4, while
preserving the atom ordering over the whole system, you can fool g_hbond
with a new .tpr without needing to touch any code. You don't even need
sensible parameters for PO4, of course.
Alternatively, adding
((*top-atoms.atomname[n])[0] == 'F') ||
to the conditional that resembles
if ((bContact ||
(((*top-atoms.atomname[n])[0] == 'O') ||
(bNitAcc ((*top-atoms.atomname[n])[0] == 'N'
ISINGRP(datable[n])) {
datable[n] |= ACC; /* set the atom's acceptor flag in
datable. */
add_acc(a,n,grp);
}
in search_acceptors() of src/gmxlib/gmx_hbond.c and recompiling is
faster still - assuming you have no other atoms whose names start with
F. For safety, name the executable something that will remind you that
it is not the standard one :-)
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond
On 31/05/2012 7:46 PM, Acoot Brett wrote: Hi Mark, It is confusing. As you know, for the same hydrogen bond in a protein, the related hydrogen bond angle and bond length can vary within a scope during the whole simulation process, however this small vibration of the hydrogen bond angle and length can lead to significant energy change, and correspondingly the energy of a hydrogen bond in simulation can be varied significantly. In comparison with hydrophobic effect, it would be too much is the energy of the hydrogen bond would be not calculated continuously. It isn't, if the model physics isn't paramtrized to include it explicitly - which is the case for all the force fields in GROMACS. Could you give some further clarification? What are trying to do? Measuring the strength of a hydrogen bond requires you identify a state with and without it and a path between them over which you can integrate. Mark Cheers, Acoot *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, 31 May 2012 4:48 PM *Subject:* Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 4:42 PM, Acoot Brett wrote: Dear All, The value of the energy of the hydrogen bond has relation with distance and angle of the hydrogen bond related atoms. As for in the simulation process, the distance and angle of the hydrogen bond related atoms may change continuously. Will you please let me know based on which formula GROMACS calculated the value of the energy of the hydrogen bonds? There is no such formula used in MD force fields implemented in GROMACS. The only non-bonded interactions are the ones you already know about: electrostatics and VDW. Observables like hydrogen bonds and the hydrophobic effect arise from them. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PME nodes
On 31/05/2012 9:11 PM, Ignacio Fernández Galván wrote: Hi all, There must be something I don't fully understand, by running grompp on a system, I get this: Estimate for the relative computational load of the PME mesh part: 0.32 Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which is the recommended value for a dodecahedral box. But then I run the dynamics with mdrun_mpi -np 8 (different cores in a single physical machine) and I get: Initializing Domain Decomposition on 8 nodes [...] Using 0 separate PME nodes I would have expected at least 2 nodes (3:1, 0.25) to be used for PME, so there's obviously something wrong in my assumption. Should I be looking somewhere in the output to find out why? Would it be better to try to get some dedicated PME node(s) (even in a single machine)? Generally mdrun does pretty well, given the constraints you've set for it. Here, you've implicitly let it choose (with mdrun -npme -1), and with fewer than a minimum number of nodes (10, in 4.5.5) it doesn't bother, since the book-keeping would be too costly. Otherwise, you can investigate the reasons for the choices mdrun made from the output in the .log file. You can try mdrun -npme 2 or 3 if you like, but it's likely not faster or might even refuse to run. See manual 3.17, also. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] (no subject)
On 31/05/2012 9:37 PM, Subramaniam Boopathi wrote: how to assign charge and charge group number when new residue as being added to the existing amino acid rtp file Read about the file format in the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About gomacs MPI installation
On 31/05/2012 10:17 PM, vidhya sankar wrote: Dear justin Thank you for your previous reply Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5) first of all i have successfully installed debain package of gromacs-openmpi for that i have configured and compiled using the following command ./configure --enable-mpi --enable-double --prefix=/usr/local/mpigromacs --program-suffix=_mpi_d then I issued the make make mdrun As you will see in the http://www.gromacs.org/Documentation/Installation_Instructions, there is no need to do both make mdrun and make because the former does part of latter. Likewise for make install-mdrun and make install. However it doesn't hurt. make install make install-mdrun It compiles nicely and successfully I have few doubt 1) should i need to install both rpm of openmpi (coresponding to my OS) and Debain of gromacs-openmpi ? (compatible to my Linux OS) Now i have both You've installed GROMACS from source already. You have no need of a binary distribution in an .rpm or .deb. However that binary probably is linked to FFTW3, which your source installation was not, so PME will likely be much faster. You should probably get rid of the source installation, and do it again following http://www.gromacs.org/Documentation/Installation_Instructions, or use the binary distribution. Otherwise is it enough to install only Debain gromacs-openmpi to install gromacs in paralleel Probably it is. 2) how to check Wheather Parallel installation of gromacs ? wheater is installed parallely or not? Something named gromacs-openmpi, or successfully configured --with-mpi is very likely to run in parallel with MPI. That's the point of the name! I have installed on single Hyper threading supported intel pentium i5 (dual core processor,four thread) it means i amusing thread based parallelism not mpi based parallelism (i know the performance may be poor, though later i will extend this to clustering) No. See http://www.gromacs.org/Documentation/Installation_Instructions. Hyper-threading is useless for GROMACS, and you have configured with MPI, which prevents attempting to use threading of any sort. please tell me The Above my understandings is correct or not if ther are any wrong things in the compilation procedure Please give me some tips to rectify error? I am very grateful to your valuable reply Also if the above procedure is correct Can i run the gromacs parallel simulation using the following command mdrun_mpi_d -nt 8 -s topol.tpr mdrun -nt is not available with an MPI-configured mdrun, and likely exits with an error. Mark Don't i Need mpirun command ? Thanks in Advance With regards S.vidhyasankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] surface tension, Long range LJ correction, TIP4P/2005
On 1/06/2012 12:18 AM, MD wrote: Hi All, I really need to know how to apply long range LJ correction to calculate surface tension of TIP4P/2005 water. I can get 65 dyn even i use vdw cut-off = 1.4 nm, but from the reference people can get 69 dyn. I included the LJ Long range LJ correction using the following .mdp, please note that i used: DispCorr = EnerPres, which means i included the long range LJ correction for energy and pressure, but why i can get only 65 dyn for surface tension. I can see Disper. corr. in the .log file, but i saw Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE That's normal for your choices of coulombtype and vdw-type. I spend two weeks on this ,but still failed to know the reason, because only myself do MD in my department. Can anyone help?? Yes. You can, by finding that 69 dyn reference and reading it :-) Nothing else is worthwhile. I'm now going to stop giving you the same advice each time you ask the same question. Mark title= Yo cpp nbsp; = /usr/bin/cpp include = define = integrator = md tinit= 0 dt = 0.001 nsteps = 500 init_step= 0 brcomm-mode= Linear nstcomm = 1 comm-grps= bd-fric = 0 ld-seed = 1993 niter= 20 nstxout = 5000 nstvout = 8000 nstfout nb sp; = 8000 nstcheckpoint= 1000 nstlog = 5000 nstenergy= 5000 nstxtcout= 500 xtc-precision= 1000 xtc-grps = energygrps = nstlist = 5 ns_type nbsp;= grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0*rvdw = 1.4 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry nb sp;= 3d epsilon_surface = 0 optimize_fft = no gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No Tcoupl = v-rescale tc-grps = System tau_t nbs p; = 0.1 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 andersen_seed= 815131 annealing= no annealing_npoints = annealing_time = annealing_temp = gen_vel = yes gen_temp = 300 gen_seed = 1993 constraints = none constraint-algorithm = Lincs unconstrained-start = no Shake-SOR= no shake-tol= 1e-04 brlincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse= no * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
On 2/06/2012 1:11 PM, Klniu wrote: Dear Gromacs users, I am doing a membrane simulation. The system are two layers composed by surfactants. other molecule are decane and water. The system like this: decane --- surfactant --- water --- surfactant --- decane My research is to get the surface tension between decane and water. I mainly use NPT simulation to reach equilibrium and product. when I set pcoupl = semiisotropic and compressibility = 4.5e-5 4.5e-5, the box at x and y will shrink incessantly and then the system crashes. My question is: 1. Is my direction of work worng? There is another way to do this simution? 2. how can I get surface tension? Equilibration with P-R pressure coupling is asking for trouble. Use Berendsen to get close, then switch. Otherwise, see http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark The content of mdp file is below: ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.0 ; long-range cut-off for switched potentials rlistlong= -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure dispcorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.135 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 1 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = -1 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = Nose-Hoover nsttcouple = -1 nh-chain-length = 10 ; Groups to couple separately tc-grps = OIL DRG SOL ; Time constant (ps) and reference temperature (K) tau_t= 0.5 0.5 0.5 ref_t= 300 300 300 ; Pressure coupling pcoupl = Parrinello-Rahman pcoupltype = semiisotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 I have post a mail in list but my description is not clear.
Re: [gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for
On 2/06/2012 7:10 PM, xi zhao wrote: Dear gmx-users: When I try to simulation a system: protein + ligand molecule using the Implicit Solvent method. the parameters of Ligand were produced by acpype, but when grompped, the appeared Velocities were taken from a Maxwell distribution at 300 K GB parameter(s) missing or negative for atom type 'o' GB parameter(s) missing or negative for atom type 'os' GB parameter(s) missing or negative for atom type 'c' GB parameter(s) missing or negative for atom type 'c3' GB parameter(s) missing or negative for atom type 'hc' GB parameter(s) missing or negative for atom type 'h1' --- Program grompp_d, VERSION 4.5.3 Source code file: grompp.c, line: 1123 Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 6 atomtypes or they might be negative. when I modified 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844amber99sbr.ff/gbsa.itp by adding the atomtype of ligand, the problem is still the same, Then you apparently didn't add them correctly. See manual section 5.3.5 and second paragraph of http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Atomtype 1
On 3/06/2012 11:03 PM, xi zhao wrote: in fact, the pdb2gmx still hang. I modified the atomtypes.atp , aminoacids.rtp , ffbonded.itp, ffnonbonded.itp , aminoacids.hdb, residuetypes.dat4 ,morever, now the pdb2gmx_d even does not the standard protein structure. So clearly you have broken the file format, probably of at least atomtypes.atp. However we can't guess how if we can't see your changes (e.g. use the diff tool). Also, you need to answer the last question Justin asked, because that answer is likely to reveal your problem... Mark --- *12?6?3?,??, Justin A. Lemkul /jalem...@vt.edu/* ??: ???: Justin A. Lemkul jalem...@vt.edu ??: Re: [gmx-users] Atomtype 1 ???: Discussion list for GROMACS users gmx-users@gromacs.org ??: 2012?6?3?,??,??8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to rename oxygen oxt to be recognized by MOLMOL
On 4/06/2012 5:00 PM, Acoot Brett wrote: Dear All, Will you please tell me how to rename the C-terminal residue atom OXT so that the OXT oxygen can be recognized by MOLMOL? You'd have to read the MOLMOL documentation. But start with O - making sure you preserve the file format correctly, probably by replacing deleted characters with spaces, for .gro or .pdb. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding error
On 4/06/2012 5:05 PM, Seera Suryanarayana wrote: Dear all gromacs users, While i am running pdb2gmx commond i am getting following error. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. I wont ignore the 22 missing atoms by using -missing commond. I would like to construct a complete protein structure.But i dont know how to construct the complete protein sturcture.Kindly tell me how to consturct the complete protein and what are the softwares i have to use here. There is no general answer to this question. You have to examine the file, see what is missing, perhaps find out why, and then perhaps use various possible solutions. Some leads are here... http://www.gromacs.org/Documentation/File_Formats/Coordinate_File Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tabulated potentials for dihedrals - regd
On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form?
On 4/06/2012 6:18 PM, Wayne Chen wrote: Hi, I'm a student at National Taiwan University doing research on protein-ligand interactions using MD simulations with GROMACS (version 4.5.3). In our simulations, we placed a protein (group A) and a ligand (group B) in a box under periodic boundary condition and ran for 20ns. I am trying to obtain snapshots of specific time frames within the trajectory file I got, but I am running into trouble outputting the exact position of the protein relative to the ligand when converting the frames into pdb files. Because of the period boundary condition, a snapshot may have the protein located on one side of the box and the ligand on the opposite end, but their actual relative positions---as measured by center of mass (COM) between specific region within the protein and the COM of the ligandare in fact much closer to each other (1.33nm as calculated by GROMACS as part of the trajectory vs. 7.585nm after being converted into a pdb file). So my question is: How do I maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form? See strategies here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Electrostatic interactions and atoms with nul charge
On 5/06/2012 12:08 AM, Laurence Leherte wrote: Dear Gromacs users, I am using the Amber99 FF in MD simulations of peptides (and proteins). In a first stage to the design a different charge distribution, most of the atomic charges were set equal to zero (i.e., all charges but the C and O backbone atoms). It appeared that the calculation times observed for the original all-atom charges and the modified system are similar. My question is thus the following one. In order to save calculation time (and whatever the FF is), how is it possible to avoid that the atoms bearing a nul charge are considered in electrostatic calculations ? I should specify here that I want these atoms to be considered in the vdW non-bonding interactions. IIRC GROMACS neighbour searching already identifies atoms with zero charge and/or LJ parameters and uses non-bonded code that does not compute contributions that are known to be zero. You should be able to see this from the differences in the flop accounting at the end of your .log files when you have different numbers of zero-charge atoms. If the total calculation times are similar, then the number of atoms for which time was saved was negligible. This would be normal for a peptide in a much larger quantity of water. You will have to judge the truth of this from the timing and flop breakdown at the end of the .log file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Writing and compiling new analyses for gromacs
On 5/06/2012 9:11 AM, Peter C. Lai wrote: The quick and dirty way is to post-patch Makefile in src/tools. I think patching the appropriate Makefile.in is sufficient for configure to pick up and automake into Makefile if all you need to do is append a make target. As to your previous question, on our cluster, I use Intel ICC 11.1.056 both openmpi and fftw3 are also built with icc but root builds those and exposes their libs/headers through Modules, so I just module load them and specify the appropriate CPPFLAGS, LDFLAGS, and MPICC to configure (I'm still on 4.5.4 here). Btw: If you are patching 4.6 you should ask for someone else on here to tell you how to add it to the CMake config, since that's going to be the default build framework going forward. That's easy with CMake - just add your tool to the list in src/tools/CMakeLists.txt and re-make (which I expect will trigger a re-cmake automatically). Mark On 2012-06-05 01:43:09AM +0300, Shay Teaching wrote: One more question: How do I get my new g_whatever analysis to be included in the compilation? Simply placing my file in src/tools won't work of course. How to I place it correctly in the build? Thanks, -Shay 2012/6/5 Justin A. Lemkuljalem...@vt.edu On 6/4/12 5:16 PM, Shay Teaching wrote: 2012/6/4 Justin A. Lemkuljalem...@vt.edumailto:jalem...@vt.edu On 6/4/12 2:59 PM, Shay Teaching wrote: Dear Gromacs users, I want to write new analyses for gromacs and compile it (so I'll have g_whatever) as part of the gromacs package. Per the instructions I found on gromacs website, I installed kdevelop and opened the gromacs as a project using kdevelop. However I have two questions: 1) When I try to compile gromacs source, through kdevelop, I get a permission denied error. I think it is because gromacs installation requires root privileges. Any suggestions on how to bypass that, so I won't have to use kdevelop as root (which is a *really* bad idea)? (e.g., installing gromacs without root?) Assuming you're trying to compile template.c in some system-level directory, you're certain to run into that problem. Compile in a different location. Actually, I tried installing Gromacs to my home directory, not system directory. You're saying that I'm not supposed to encounter this error? You shouldn't have permission errors in your home directory. I've never used KDevelop; what happens if you try to compile from a normal command line? 2) Are there any guidelines for writing new g_whatever analyses? Or any general suggestions on how to approach it? Write good code? ;) I don't really know what you're asking here, but if you want pointers for writing code, you'll need to at least state what you're doing. Write good code of course :-) What I mean is: Is there a proper list of gromacs functions used for 'common' operations? (such as, reading from trajectory, reading index file, documentation of types and data structures for dealing with gromacs trajectory: atom, molecule, their input and output, etc.) Of course I'll open existing analyses, and see how its done there (g_mindist, g_rms..) but it would be useful to have like... a list of methods so I won't waste time on stuff that's already been dealt with. The only related information is probably on the website at http://www.gromacs.org/**Developer_Zone/Programming_**Guidehttp://www.gromacs.org/Developer_Zone/Programming_Guide. I doubt you'll get a how-to for coding though. The approach of looking at existing files for these routines is probably as efficient as it gets. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing
