[gmx-users] Umbrella Sampling - NPT
Dear Justin, I am wondering whether in NPT simulations before umbrella sampling in each window the option: continuation = yes should be set to continuation = no as you provided 1st option. Thank you, Steven -- 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] cannot determine precision of trn file
Dear All, I was running my simulation for 30ns but at the last step i got following error: Cannot close energy file;it might be corrupt, or maybe you are out of quota. It was found that there was some disk space problem but when the issue was resolved i restarted my run from the last step using append option in mdrun. When finally the *.trr was created i used gmxcheck -f *.trr. But then i got error saying that Cannot determine precision of trn file.I have checked my state.cpt and *.log file, they have correct number of frames.But then why *.trr is giving this error. Please Help.Thank you 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. 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] Distance between selected atoms during simulation
Dear Gromacs Users! I want to perform measurements of the distances between backbone as well as side-chain atoms of the selected residues using gro and trajectory files. What Gromacs program should I use for such measurements? James -- 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] cannot determine precision of trn file
On 5/03/2012 8:48 PM, Nidhi Katyal wrote: Dear All, I was running my simulation for 30ns but at the last step i got following error: Cannot close energy file;it might be corrupt, or maybe you are out of quota. It was found that there was some disk space problem but when the issue was resolved i restarted my run from the last step using append option in mdrun. When finally the *.trr was created i used gmxcheck -f *.trr. But then i got error saying that Cannot determine precision of trn file.I have checked my state.cpt and *.log file, they have correct number of frames.But then why *.trr is giving this error. IIRC there's some magic numbers that get written to the start of each frame that allow the reading software to determine the precision on the fly. It seems your .trr file lacks these. Maybe your file system and/or attempts at re-starts have not dealt well with the lack of available disk space. If you were able to restart, then the .trr was fine up to the restart point, but it is not clear from the above whether you did achieve a restart... 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] Distance between selected atoms during simulation
On 5/03/2012 8:48 PM, James Starlight wrote: Dear Gromacs Users! I want to perform measurements of the distances between backbone as well as side-chain atoms of the selected residues using gro and trajectory files. What Gromacs program should I use for such measurements? Check out manual section 7.4 for clues, chapter 8 for more info, and Appendix D for nuts and bolts. Learning to use the free resources that people have already given you is an efficient use of everyone's 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
[gmx-users] Simple LJ system
I have literally just started using gromacs and hopefully have a pretty straight forward question. Firstly I am interested in simulating a binary Lennard-jones system with arbitrary choices of parameters (i.e. I may choose the epsilon and sigma). If someone could summarise what ingredients I would need for this it would be greatly appreciated. My current understanding of topology files and .itp files is fairly limited so a comprehensive reply will be very much appreciated. Thank you in advance, Jeff Armstrong -- Jeff Armstrong Department of Chemistry, Imperial College, SW7 2AZ, London, United Kingdom -- 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: Gromacs-GPU benchmark test killed after exhausting the memory
Hi Efrat, It indeed looks like a memory leak. Could you please file a bug on redmine.gromacs.org? Cheers, -- Szilárd On Sun, Mar 4, 2012 at 12:21 PM, Efrat Exlrod efrat.exl...@biu.ac.il wrote: Hi Szilard, Thanks for your reply. I used your script and I think it does look as a memory leak. Please look at the attached runchkmem.out Is it possible this problem exists in version 4.5.5 and was solved in version 4.6 you are using? When will version 4.6 be released? Thanks, Efrat Message: 2 Date: Fri, 2 Mar 2012 14:46:25 +0100 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cannyew7rxa0nz2weuymwhzucmfm2k6jyyp1htwghcbadtvd...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, First I thought that there might be a memory leak which could have caused this if you ran for really long time. However, I've just ran the very same benchmark (dhfr with PME) for one hour, monitored the memory usage and I couldn't see any change whatsoever (see the plot attached). I've attached a script I used to monitor the memory usage, feel free to use if you want check again. Cheers, -- Szil?rd On Wed, Feb 29, 2012 at 9:50 AM, Efrat Exlrod efrat.exl...@biu.ac.il wrote: Hi, I have?Gromacs-GPU version 4.5.5 and?GTX 580. I ran?dhfr-solv-PME benchmark test (see below) and my run was killed after couple of hours?exhausting all the computer memory, including the swap (2G +?4G swap). Has anyone encountered this problem? What?is wrong? Thanks, Efrat -- 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
[gmx-users] [ bondedtypes ]
Thanks for your help. :-) I did not realize that table 5.5 corresponds to [ bondedtypes ] 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
[gmx-users] a warning in grompp
dear all; I am trying to run grompp command and I encounter this: . WARNING 1 [file topol.top, line 54]: The bond in molecule-type DNA_chain_A between atoms 1 H5T and 2 O5' has an estimated oscillational period of 9.0e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. however when I use -maxwarn with grompp, it seems like that there is nothing wrong. Is it OK to continue the simulation with using maxwarn, or is there some thig wrong that needs to be modified? Thank you in advance Banafsheh -- 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] How to answer in this mailing list?
Hello I wrote an email to the mailing list with the subject [ bondedtypes ] and I got answers that helped me. I wanted to answer to this by a new email with same subject and the mailing list create a new question out of it. How do I answer in this mailing list to a topic? Thanks 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
[gmx-users] g_msd segmentation fault
Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4 Selected 4: 'SOL' Split group of 16800 atoms into 480 molecules trn version: GMX_trn_file (double precision) Reading frame 800 time 4.000 Segmentation fault However when I perform the same analysis on the solute molecules it runs to completion. I have checked the configuration of the system at frame 800 and everything seems to be fine. I have also analysed the energy and there seems to be no problem. Has anybody any idea of what might be happening? Cheers Gavin -- 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 warning in grompp
Banafsheh Mehrazma wrote: dear all; I am trying to run grompp command and I encounter this: . WARNING 1 [file topol.top, line 54]: The bond in molecule-type DNA_chain_A between atoms 1 H5T and 2 O5' has an estimated oscillational period of 9.0e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. however when I use -maxwarn with grompp, it seems like that there is nothing wrong. Is it OK to continue the simulation with using maxwarn, or is there some thig wrong that needs to be modified? Don't believe that nothing is wrong when using -maxwarn. If you're invoking -maxwarn, you're telling grompp ignore all the things you think are problems. Unless you understand the exact implications of overriding these warnings, you shouldn't be blindly pushing forward. As the warning states, your time step is too long to be stable in the absence of constraints. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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 answer in this mailing list?
On 5/03/2012 11:39 PM, Lara Bunte wrote: Hello I wrote an email to the mailing list with the subject [ bondedtypes ] and I got answers that helped me. I wanted to answer to this by a new email with same subject and the mailing list create a new question out of it. How do I answer in this mailing list to a topic? Choosing reply in your email client is the normal way. The fact that this is a mailing list and not a normal email exchange should be transparent to you ... unless one has chosen to receive digests. In that case the normal procedure seems to be to just reply anyway and leave one's readers to work out the subject about which one is talking, rather than editing the subject and removing the extraneous material that confuses search tools :-P 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] g_msd segmentation fault
On 5/03/2012 11:39 PM, Gavin Melaugh wrote: Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4 Selected 4: 'SOL' Split group of 16800 atoms into 480 molecules trn version: GMX_trn_file (double precision) Reading frame 800 time 4.000 Segmentation fault However when I perform the same analysis on the solute molecules it runs to completion. I have checked the configuration of the system at frame 800 and everything seems to be fine. I have also analysed the energy and there seems to be no problem. Has anybody any idea of what might be happening? Running out of memory would be the first suggestion. A segmentation fault is a generic error message when a C program (ie. GROMACS) has assumed that it can get access to a certain amount of memory, but is in fact doing so in a way that breaks the rules that segment memory so that one (part of a) program can't hurt another one. Running in single precision will roughly halve your memory requirements, probably without affecting your results. Reducing the number of frames can help also, but it seems you already have fairly few frames. Using -mol probably increases the amount of memory you need by an amount proportional to the number of such molecules (or maybe its square?). 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 answer in this mailing list?
Hi Thanks for answer. This is also a test if it work :-) 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] Simple LJ system
Jeff Armstrong wrote: I have literally just started using gromacs and hopefully have a pretty straight forward question. Firstly I am interested in simulating a binary Lennard-jones system with arbitrary choices of parameters (i.e. I may choose the epsilon and sigma). If someone could summarise what ingredients I would need for this it would be greatly appreciated. My current understanding of topology files and .itp files is fairly limited so a comprehensive reply will be very much appreciated. You can follow a similar force field structure like any of the ones that already exist in Gromacs, except that you don't need any bonded parameters. You need a [defaults] directive to define interaction types, [atomtypes] to define the nonbonded parameters of your species, and then you can proceed to the [moleculetype] and [atoms] levels. All of this can be done within a unified .top, or you can create your own custom force field that can be #included within other topologies, making your own forcefield.itp (to have the [defaults] and any necessary #include statements) and ffnonbonded.itp for the [atomtypes]. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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: how modify the forcefield amino acid definitions for non-naturally occuring amino acids?
Kirill Bessonov wrote: Thank you Justin for your prompt reply, as usual :) With the last 2 lines of my previous post, I was referring on how to build *.itp files for completely new molecules (say lipids such as DMPC, DMPE or glutathione) that are not defined in the forcefield. I.e. how to derive dihedral angle code, force constant, etc. so that this new molecules could be used in the simulation. I.e. how to build your own *.itp and *.top files. Or better said, how the parameters for already defined molecules in the forcefield, such as amino-acids and ions were created? Where can we get more information about this ins and outs of building your own topologies? Maybe there are some good references that you can refer me? Read the primary literature for whatever force field(s) you're interested in. Parameterization methodology should be present in the original publications or any that refer to modifications of the original parameter set. Details can be sketchy depending on the force field, so be prepared to invest significant time in this endeavor. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] Umbrella Sampling - NPT
Steven Neumann wrote: Dear Justin, I am wondering whether in NPT simulations before umbrella sampling in each window the option: continuation = yes should be set to continuation = no as you provided 1st option. The starting structures were the product of simulations that were previously conducted using constraints, so in that case, the distinction between the two is probably irrelevant. You should do whatever makes the most physical sense in your case. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] g_msd segmentation fault
On Mon, 2012-03-05 at 23:56 +1100, Mark Abraham wrote: On 5/03/2012 11:39 PM, Gavin Melaugh wrote: Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4 Selected 4: 'SOL' Split group of 16800 atoms into 480 molecules trn version: GMX_trn_file (double precision) Reading frame 800 time 4.000 Segmentation fault However when I perform the same analysis on the solute molecules it runs to completion. I have checked the configuration of the system at frame 800 and everything seems to be fine. I have also analysed the energy and there seems to be no problem. Has anybody any idea of what might be happening? Running out of memory would be the first suggestion. A segmentation fault is a generic error message when a C program (ie. GROMACS) has assumed that it can get access to a certain amount of memory, but is in fact doing so in a way that breaks the rules that segment memory so that one (part of a) program can't hurt another one. Running in single precision will roughly halve your memory requirements, probably without affecting your results. Reducing the number of frames can help also, but it seems you already have fairly few frames. Using -mol probably increases the amount of memory you need by an amount proportional to the number of such molecules (or maybe its square?). Mark However, it seems that the mol flag of g_msd is still buggy as described by: http://redmine.gromacs.org/issues/774 Unfortunately, this bug is still not fixed, though a patch seems to be provided. My workaround for this problem is to convert the trajectory with trjconv using the flag -pbc whole and apply g_msd without the -mol option, but providing appropriate index groups for every single molecule. Unfortunately, this method is very time consuming, because the trajectory has to be read, many many times. Afterwards, I just average the results for the different molecules and derive the diffusion coefficient from the averaged MSD. /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] cannot determine precision of trn file
I think my restart was achieved successfully as my err file contained following lines: reading checkpoint file state.cpt generated: Loaded with memory making 2D domain decomposition 4*2*1 starting mdrun 'protein in water' 1500 steps, 3.0ps(continuing from step 1500, 3.0ps). Also .log file is giving me correct number of frames but when i checked .ene file it says: There may be something wrong with energy file .ene Found: step=0,nre=0,ndisre=0,nblock=0,time=0 Trying to skip frame expect a crash though . . . Timesteps at t=0 don't match (0,11470) timesteps at t=11470 don't match (11470,10) last energy frame read 3057 time 3.002 found 3058 frames I think the problem is arising since the operating system crashed when the .ene file is still open in memory and so even .trr file was not created sucessfully. Can you please suggest me the solution to the problem without having to restart my run from the very beginning. Thank you 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. 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: Lennard-Jones Interactions in Gromacs
Please make sure to send replies to the list (gmx-users@gromacs.org) rather than my personal inbox. Lara Bunte wrote: Hi Thank you for helping me. I still don't get it. Out of the support of charmm force field I have a document with following parameters: ATOM NAMEATOM TYPE epsilon ( kcal ,mole^-1) sigma (Angstrom) Notes O1 O -0.12 1.700 Oleamide and so on, a hole list of such information. How and where do I give this information to gromacs? Could you give me just one line example syntax? Look in ffnonbonded.itp, in the [atomtypes] directive. The format and contents of this directive are explained in the manual. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] Imitation of the protein part
Hi Gmx Users, I am simulationg parts of the big protein so in this case imitating non charged terminals. For this purpose I use option: pdb2gmx -f Protein.pdb -ter Which option would be suitable and safe to imitate it: a) NH2 and COOH b) None Thank you! Steven -- 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] Acpype Parameter Error?
Kyle, can you send and pdb file so I can reproduce your issue? Thanks, Alan On 24 February 2012 23:25, Kyle Greenway kgree...@sfu.ca wrote: Hello, This email is directed mainly to Alan, who created Acpype. I've noticed that Acpype has assigned dihedral constants as 0.65084 for many dihedrals of the form X -c3-n4-X, X -c3-c3-X, and others, in my generated GROMACS .itp files. These dihedrals have values of 1.400 in the amber 99sb .dat file, which should have instead given 1.4*4.184 = 5.858 for the result. Most other dihedrals I've checked have behaved normally and their values correspond to what would be expected - except for dihedrals with values of 0.65084 in the .itp files. Any ideas about what's going on? Thanks for your time. Kyle Greenway -- 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 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] segmentation fault err
Dear gmx-users, I'm facing segmentation fault error while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values, potential energy etc. are not changing much so i guess this is the cause for fatal error. But I can't figure out the reason behind sudden increase in temperature. I'm using following options in my mdp file: ;Temperature coupling tc-grps = system tau_t = 1.0 ; Temperature coupling time constant. ref_t = 50.0 ; In reduced units ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 50.0 Can anybody suggest me, if i'm missing something (to take care of)? Regards, Shilpa -- 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] folding of coordinates in trajectory files
Hi All I was wondering. I assume gromacs writes folded coordinates in the trajectory files. If so does it use rx(i) = rx(i) -boxl *nint(rx(i) / boxl) to fold the coordinates at each step? and where does it define the origin (0,0,0) Cheers Gavin -- 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] Imitation of the protein part
Specifying none for the termini, in conjunction with suitable capping groups to create uncharged peptide bonds at the termini (which have to be built on with external software), is the best approach to modeling such a system, in my opinion. -Justin Steven Neumann wrote: Hi Gmx Users, I am simulationg parts of the big protein so in this case imitating non charged terminals. For this purpose I use option: pdb2gmx -f Protein.pdb -ter Which option would be suitable and safe to imitate it: a) NH2 and COOH b) None Thank you! Steven -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] segmentation fault err
On 6/03/2012 2:58 AM, shilpa yadahalli wrote: Dear gmx-users, I'm facing segmentation fault error while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values, potential energy etc. are not changing much so i guess this is the cause for fatal error. But I can't figure out the reason behind sudden increase in temperature. I'm using following options in my mdp file: ;Temperature coupling tc-grps = system tau_t = 1.0 ; Temperature coupling time constant. ref_t = 50.0 ; In reduced units ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 50.0 Can anybody suggest me, if i'm missing something (to take care of)? You will need to look at the end of the .log and/or stdout file to know, but probably this is what is happening http://www.gromacs.org/Documentation/Terminology/Blowing_Up 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] folding of coordinates in trajectory files
Hey Gavin, still can't get the binary system to run. if I give you the files I am using could you have a quick peak and see if I am doing anything obviously wrong? Jeff -- Jeff Armstrong Department of Chemistry, Imperial College, SW7 2AZ, London, United Kingdom -- 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] folding of coordinates in trajectory files
On 6/03/2012 2:59 AM, Gavin Melaugh wrote: Hi All I was wondering. I assume gromacs writes folded coordinates in the trajectory files. If so does it use rx(i) = rx(i) -boxl *nint(rx(i) / boxl) to fold the coordinates at each step? and where does it define the origin (0,0,0) GROMACS suits itself, and I don't believe there is a simple way to write what down what it produces. 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] cannot determine precision of trn file
On 6/03/2012 12:30 AM, Nidhi Katyal wrote: I think my restart was achieved successfully as my err file contained following lines: reading checkpoint file state.cpt generated: Loaded with memory making 2D domain decomposition 4*2*1 starting mdrun 'protein in water' 1500 steps, 3.0ps(continuing from step 1500, 3.0ps). Also .log file is giving me correct number of frames but when i checked .ene file it says: There may be something wrong with energy file .ene Found: step=0,nre=0,ndisre=0,nblock=0,time=0 Trying to skip frame expect a crash though . . . Timesteps at t=0 don't match (0,11470) timesteps at t=11470 don't match (11470,10) last energy frame read 3057 time 3.002 found 3058 frames I think the problem is arising since the operating system crashed when the .ene file is still open in memory and so even .trr file was not created sucessfully. Can you please suggest me the solution to the problem without having to restart my run from the very beginning. Thank you in advance You can only restart from a .cpt frame, and that will only be useful if the trajectory frames before it are not corrupted. -- 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] em.mdp file
Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 Thanks for help 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] em.mdp file
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Lara Bunte [lara.bu...@yahoo.de] Sent: Monday, March 05, 2012 5:24 PM To: gmx-users@gromacs.org Subject: [gmx-users] em.mdp file Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 Thanks for help Greetings Lara This file is for energy minimization rather than for a MD run. Start reading Manual together with Justin's tutorials to clarify the basics: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ Jan -- 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] em.mdp file
Lara Bunte wrote: Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 You should set nstlist=1 for energy minimization (which is not, by definition, MD). -Justin rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 Thanks for help Greetings Lara -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] em.mdp file
Justin A. Lemkul wrote: Lara Bunte wrote: Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 You should set nstlist=1 for energy minimization (which is not, by definition, MD). Hit send too soon... You have also specified 200 steps. This seems arbitrary to me, as there is no guarantee that EM will be done at that point. You also need to specify a value for emtol and emstep to be more effective. There are tutorials linked from the Gromacs webpage. I'd suggest you work through at least one or two of them to understand what the .mdp files are trying to achieve and what a proper workflow might be. -Justin rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 Thanks for help Greetings Lara -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] grompp error - bondedtypes
Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and get this errors: ERROR 1 [file flavin.rtp, line 1]: Invalid directive bondedtypes ERROR 2 [file flavin.rtp, line 7]: Not enough parameters I know where this error occurs from but I don't know what is false. Could you please take a look on my files, see appendix. Thanks Greetings Lara topol.top Description: Binary data flavin.rtp Description: Binary data -- 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 - bondedtypes
Lara Bunte wrote: Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and get this errors: ERROR 1 [file flavin.rtp, line 1]: Invalid directive bondedtypes ERROR 2 [file flavin.rtp, line 7]: Not enough parameters I know where this error occurs from but I don't know what is false. Could you please take a look on my files, see appendix. grompp should never read .rtp files, so somewhere in your files you're likely trying to #include it or otherwise invoke it. There is no indication of this in your topology, so we can't tell where the error is. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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 - bondedtypes
Lara Bunte wrote: Yes it was included in forcefield.itp Only pdb2gmx uses .rtp files (see the manual). Thanks for your help Know I got the error No default Fourier Dih. types What should I do? You need a corresponding [dihedraltypes] for all dihedrals in the system. The error indicates there is a dihedral for which parameters do not exist. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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:Re: [gmx-users] grompp error - bondedtypes
Justin A. Lemkul jalem...@vt.edu wrote: Lara Bunte wrote: Yes it was included in forcefield.itp Only pdb2gmx uses .rtp files (see the manual). Thanks for your help Know I got the error No default Fourier Dih. types What should I do? You need a corresponding [dihedraltypes] for all dihedrals in the system. The error indicates there is a dihedral for which parameters do not exist. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] a question related to MD by gromacs
Dear All, I plan to do 1 ns MD for a protein with MW 50, 000 by gromacs. As for my gromacs was installed in the cygwin by a laptop, I cannot run it day and night, which means my 1 ns MD needs to have a lot of stops and restart. Will you please remind me the gromacs command to reinstiate the gromacs after it has stopped for example at 0.1 ns, which means I will restart from 0.1 ns? I am looking forward to getting a reply from you. Cheers, Dialing -- 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 question related to MD by gromacs
Dialing Pretty wrote: Dear All, I plan to do 1 ns MD for a protein with MW 50, 000 by gromacs. As for my gromacs was installed in the cygwin by a laptop, I cannot run it day and night, which means my 1 ns MD needs to have a lot of stops and restart. Will you please remind me the gromacs command to reinstiate the gromacs after it has stopped for example at 0.1 ns, which means I will restart from 0.1 ns? http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] spatial distribution function
I am trying to calculate spatial distribution function (SDF) for ionic liquid.I want to see the distribution of anion around cation. I followed the steps given in gromacs manual.I created two groups each of single cation and all anions in the index file and did two steps trjconv_d to get trajectory for centered solute by removing translational and rotational degrees of freedom. When I am running g_spatial_d on this trajectory I am only able to see anions in my cube file as I am selecting anions for writing output co-ordinates. Am I following correctly or doing something wrong ? I am using updated gromacs version 4.5.4. Please I would really appreciate if someone can help this? Thank you in advance. Pre ---BeginMessage--- Hello everyone, I am trying to calculate spatial distribution function (SDF) for ionic liquid.I want to see the distribution of anion around cation. I followed the steps given in gromacs manual.I created two groups each of single cation and all anions in the index file and did two steps trjconv_d to get trajectory for centered solute by removing translational and rotational degrees of freedom. When I am running g_spatial_d on this trajectory I am only able to see anions in my cube file as I am selecting anions for writing output co-ordinates. Am I following correctly or doing something wrong ? I am using updated gromacs version 4.5.4. Please I would really appreciate if someone can help this? Thank you in advance. Prema. ---End Message--- -- 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
