[gmx-users] Re: how modify the forcefield amino acid definitions for non-naturally occuring amino acids?
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? -- 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] Re: Test particle insertion extra coordinate
Thank you so much for taking the time to look at the code. That should work, I will try it. -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546442.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] Re: Test particle insertion extra coordinate
The error is correct. After inspecting the code, the extra coordinate (coordinate of the cavity) is taken from the last atom of the trajectory (rerun_fr.x) and not from the .tpr file (mdatoms). This is weird, but allows different cavities for different frames I guess... I am guessing you can add the extra coordinate (cavity coordinate) to each frame. You just need to convert from a binary version (.xtc, .trr) to a ascii version (.gro, .g96), add the coordinate, convert back to binary (optional, but saves space), and make the rerun over this. Be _careful_ with the conversions not to screw the original trajectory. Plus, with this, there is no need for topology mambo-jambos (calling CL- to the cavity location, etc). I did not remember this because I hacked the code and I bypass that part, giving the extra coordinate (cavity) through a variable. I hope this solves your problem. Best, João On Sun, Mar 4, 2012 at 11:54 PM, MPID wrote: > Thanks a lot for the reply! I did as you said. I had a coordinate file > where > I wanted to add insert a water molecule withing a cavity. I added these > lines to the .gro file: > 340SOL OW 1274 2.925 0.061 2.677 0.2533 -0.1222 0.1294 > 340SOLHW1 1275 2.893 0.000 2.605 -0.1856 0.5697 -0.2686 > 340SOLHW2 1276 2.849 0.082 2.739 0.5491 -0.4502 0.6106 > 341INS X 2036 0.000 0.000 1.000 0. 0. 0. > I realize I still neeed to center the water molecule, but I am testing now. > To make grompp work, I added a line in the .top file and called the last > coordinate a CL- atom. I then can do grompp. But when I do mdrun -rerun, I > get this error: > Fatal error: > Number of atoms in trajectory (2032) minus one is not equal the number in > the run input file (2036) minus the number of atoms to insert (1) > The math here seems to imply that the extra atom belongs in the trajectory > rather than the tpr file, and also, it now thinks I'm inserting a CL- atom > instead of water. > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546192.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 > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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] Re: Test particle insertion extra coordinate
Thanks a lot for the reply! I did as you said. I had a coordinate file where I wanted to add insert a water molecule withing a cavity. I added these lines to the .gro file: 340SOL OW 1274 2.925 0.061 2.677 0.2533 -0.1222 0.1294 340SOLHW1 1275 2.893 0.000 2.605 -0.1856 0.5697 -0.2686 340SOLHW2 1276 2.849 0.082 2.739 0.5491 -0.4502 0.6106 341INS X 2036 0.000 0.000 1.000 0. 0. 0. I realize I still neeed to center the water molecule, but I am testing now. To make grompp work, I added a line in the .top file and called the last coordinate a CL- atom. I then can do grompp. But when I do mdrun -rerun, I get this error: Fatal error: Number of atoms in trajectory (2032) minus one is not equal the number in the run input file (2036) minus the number of atoms to insert (1) The math here seems to imply that the extra atom belongs in the trajectory rather than the tpr file, and also, it now thinks I'm inserting a CL- atom instead of water. -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546192.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] Re: Test particle insertion extra coordinate
Hello MPID (?), Sorry, I did not see your first message. For the tpic algorithm, the coordinate of insertion is the last coordinate (after the particle to be inserted) in the .tpr you give for the mdrun -rerun. Hence, you should create a structure file (.gro) with the original system, followed by the particle to be inserted, and lastly, the coordinate of insertion. Run this structure file through grompp to generate a .tpr file, which you shall give to mdrun. I hope this has helped. Best, João On Sun, Mar 4, 2012 at 10:43 PM, MPID wrote: > If no one knows this, does anyone know the best way to add a coordinate to > a > trajectory in general? > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546083.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 > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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] Re: Test particle insertion extra coordinate
If no one knows this, does anyone know the best way to add a coordinate to a trajectory in general? -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546083.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] Amber99bsc0
It is possible but not yet included in Gromacs. As far as I know, there are several people working on porting this forcefield to Gromacs (I have been searching for this myself last year). Check the archives for parmbsc0 and Gromacs and search for papers that include these terms. then you will find some of them. Maybe they will help you if you ask kindly. As an alternative, you can try using ACPYPE. Best regards, Matthias On 04.03.2012 17:32, Amir Abbasi wrote: Hi! I want to use amber99bsc0 in gromacs. is it possible? thanks. -- 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 modify the forcefield amino acid definitions for non-naturally occuring amino acids?
Kirill Bessonov wrote: Dear Gmx users, I had been using Gromacs for couple of years and always found these forums quite helpful. Right now again I have another question to ask that I was not able to figure out yet myself and reading previous posts. I need to the ffG53a6 forcefield to be able to recognize the non-standard amino acid like AZE (Azetidine-2-carboxylic acid) which closely resembles Proline, but lacks CH2 group in the ring of the side-group, making the R-group a 4 member ring instead of 5. Thus, this amino acid has very close chemical structure to the Proline which is properly defined in the *.rtp file as below [ PRO ] [ atoms ] N N 0.0 0 CA CH1 0.0 1 CB CH2R 0.0 1 CG CH2R 0.0 2 CD CH2R 0.0 2 C C 0.450 3 O O -0.450 3 [ bonds ] NCAgb_21 NCDgb_21 CACBgb_27 CA Cgb_27 CBCGgb_27 CGCDgb_27 C Ogb_5 C+Ngb_10 [ angles ] ; aiajak gromos type -C NCA ga_31 -C NCD ga_31 CA NCD ga_21 NCACB ga_13 NCA C ga_13 CBCA C ga_13 CACBCG ga_13 CBCGCD ga_13 NCDCG ga_13 CA C O ga_30 CA C+N ga_19 O C+N ga_33 [ impropers ] ; aiajakal gromos type N-CCACD gi_1 CA N CCB gi_2 CCA+N O gi_1 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 CA NCDCG gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCGCD gd_34 CBCGCD N gd_34 The question is how can I derive from this Proline definition topology the corresponding topology for AZE? The problem is that I do know how to You can use PRO as a framework, but you'll likely have to define completely new angle and dihedral terms for the four-membered ring. No such group exists in normal biomolecules, so likely the force field cannot handle it without modification. interpret the each column such as the "gromos definition" column gd_14, etc, as well as other columns. Where can I get information or tutorials about this important issue on how to create own topology files? Maybe someone can explain those columns in easy terms? What are The terms are defined in ffbonded.itp: ; Dihedral-angle type code ; Force constant ; Phase shift ; Multiplicity ; Example of usage in terms of non-bonded atom types ; ; ; ICP(H)[N] CP[N] PD[N] NP[N] ; #define gd_1180.000 2.67 1 ; CHn-CHn-CHn-OA (sugar) 0.6 Therefore, gd_1 is the type code, 180.000 is the force constant, 2.67 is the phase shift, and 1 is the multiplicity. The comment line below this definition is its example usage in terms of standard atom types/functional groups. corresponding atoms referred by atom names in the final structure as the there is not ASCI diagram of those as I've seen in AMBER tutorials? The atom names used are standard nomenclature for amino acids. Also I am interested in knowing on how the topology files are created from scratch? Sorry, I don't understand what you mean here. -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] Is TRO defined correctly in the ffG43a1p forcefield file?
Kirill Bessonov wrote: Dear all, I am trying to run simulation with phosphorylated Threonine (TRO) and I found lot's of info about this issue reading previous posts which explained on how to patch the force-field files and define this modified amino acid. After looking at the community forcefield offered here http://www.gromacs.org/Downloads/User_contributions/Force_fields After exploring those files what calls my attention is that in the *.hdb file that describes which atoms are protonated is seems to have an issue that I wanted to double-check with the rest of the members. It seems to me that the CH3 group is not protonated in the phosphotyrosine (TRO) as shown below Extracted from *.hdp file THR 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA TPO 1 1 1 H N -C CA ...but where is the 2nd line??? Why THR has 2 lines why the TRO having the PO3 group has only one line? Can somebody explain this? There is only one polar H in TPO. Read the .rtp entry for TPO - it states that it is the -2 form of the phosphorylated residue. The HG1 atom connected to OG1 is removed with the formation of a phosphoester in the modified sidechain. TPOH is the -1 form of the phosphate and thus there is a proton on the phosphate group. -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] Is TRO defined correctly in the ffG43a1p forcefield file?
Dear all, I am trying to run simulation with phosphorylated Threonine (TRO) and I found lot's of info about this issue reading previous posts which explained on how to patch the force-field files and define this modified amino acid. After looking at the community forcefield offered here http://www.gromacs.org/Downloads/User_contributions/Force_fields After exploring those files what calls my attention is that in the *.hdb file that describes which atoms are protonated is seems to have an issue that I wanted to double-check with the rest of the members. It seems to me that the CH3 group is not protonated in the phosphotyrosine (TRO) as shown below Extracted from *.hdp file THR 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA TPO 1 1 1 H N -C CA ...but where is the 2nd line??? Why THR has 2 lines why the TRO having the PO3 group has only one line? Can somebody explain this? Kirill -- 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 modify the forcefield amino acid definitions for non-naturally occuring amino acids?
Dear Gmx users, I had been using Gromacs for couple of years and always found these forums quite helpful. Right now again I have another question to ask that I was not able to figure out yet myself and reading previous posts. I need to the ffG53a6 forcefield to be able to recognize the non-standard amino acid like AZE (Azetidine-2-carboxylic acid) which closely resembles Proline, but lacks CH2 group in the ring of the side-group, making the R-group a 4 member ring instead of 5. Thus, this amino acid has very close chemical structure to the Proline which is properly defined in the *.rtp file as below [ PRO ] [ atoms ] N N 0.0 0 CA CH1 0.0 1 CB CH2R 0.0 1 CG CH2R 0.0 2 CD CH2R 0.0 2 C C 0.450 3 O O -0.450 3 [ bonds ] NCAgb_21 NCDgb_21 CACBgb_27 CA Cgb_27 CBCGgb_27 CGCDgb_27 C Ogb_5 C+Ngb_10 [ angles ] ; aiajak gromos type -C NCA ga_31 -C NCD ga_31 CA NCD ga_21 NCACB ga_13 NCA C ga_13 CBCA C ga_13 CACBCG ga_13 CBCGCD ga_13 NCDCG ga_13 CA C O ga_30 CA C+N ga_19 O C+N ga_33 [ impropers ] ; aiajakal gromos type N-CCACD gi_1 CA N CCB gi_2 CCA+N O gi_1 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 CA NCDCG gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCGCD gd_34 CBCGCD N gd_34 The question is how can I derive from this Proline definition topology the corresponding topology for AZE? The problem is that I do know how to interpret the each column such as the "gromos definition" column gd_14, etc, as well as other columns. Where can I get information or tutorials about this important issue on how to create own topology files? Maybe someone can explain those columns in easy terms? What are corresponding atoms referred by atom names in the final structure as the there is not ASCI diagram of those as I've seen in AMBER tutorials? Also I am interested in knowing on how the topology files are created from scratch? Any help will be greatly appreciated. Kirill -- 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] Advice on High Precision Structure File Formats
Tot Ziens! Op 4 mar 2012 om 18:44 heeft "Andrew DeYoung" het volgende geschreven: > Hi, > > If you have time, I would be grateful for any advice you have about which > structure file format that I should use. I am attempting to create a carbon > nanotube. However, the carbon-carbon bond length that I would like to use > is 0.1415 nm, which means that I would like a structure file format that can > take positions up to accuracies of at least 0.0001 nm. > > Unfortunately, the .gro file format only accepts positions up to accuracies > of 0.001 nm. This means that if I use .gro, I will need to round the > carbon-carbon bond length to 0.142 nm or 0.141 nm, which I would prefer not > to do. > > Now, I know that the Gromacs code itself uses many more decimal places > internally for running MD (single precision give a lot of decimal places and > double precision gives even more). I think this means that if I specify the > carbon-carbon bond length in my topology as 0.1415 nm in [ bonds ] (and the > .itp file format, and others, allow this type of precision) then even if I > must use 0.142 nm in my starting configuration .gro file, the bond lengths > will equilibrate to ~0.1415 nm if I run a short simulation (given that the > Gromacs code internally uses high precision). > > Yet, what if I need my starting configuration to have high precision bond > lengths (0.1415 nm)? I plan to freeze the carbon atoms using a freeze > group, and it would be easiest if I could do this from the get-go (i.e., > without running equilibration in which the carbon atoms are unfrozen). > > Do you have any advice about which file format I should use? I need not be > "constrained" by .gro > (http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_ne > ed_for_a_.gro_file). > G96 > .pdb, it seems > (http://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)#Example), > gives position precision up to 0.001 ANGSTROM (or 0.0001 nm), which means > .pdb will give me just enough precision. Or should I instead write my > starting configuration in a .g96 file, which allows very high position > precision? However, other than > http://manual.gromacs.org/current/online/g96.html, I am having some > difficulty (even with Google) locating detailed information about the .g96 > file format. Unfortunately, my institution I do not think has a GROMOS-96 > license, so I cannot access its manual. > > Between .pdb and .g96, which would you recommend? Or is there any other > structure file format that I am not thinking of? > > Thanks so much. > > Andrew DeYoung > Carnegie Mellon University > > -- > 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] Advice on High Precision Structure File Formats
Hi, If you have time, I would be grateful for any advice you have about which structure file format that I should use. I am attempting to create a carbon nanotube. However, the carbon-carbon bond length that I would like to use is 0.1415 nm, which means that I would like a structure file format that can take positions up to accuracies of at least 0.0001 nm. Unfortunately, the .gro file format only accepts positions up to accuracies of 0.001 nm. This means that if I use .gro, I will need to round the carbon-carbon bond length to 0.142 nm or 0.141 nm, which I would prefer not to do. Now, I know that the Gromacs code itself uses many more decimal places internally for running MD (single precision give a lot of decimal places and double precision gives even more). I think this means that if I specify the carbon-carbon bond length in my topology as 0.1415 nm in [ bonds ] (and the .itp file format, and others, allow this type of precision) then even if I must use 0.142 nm in my starting configuration .gro file, the bond lengths will equilibrate to ~0.1415 nm if I run a short simulation (given that the Gromacs code internally uses high precision). Yet, what if I need my starting configuration to have high precision bond lengths (0.1415 nm)? I plan to freeze the carbon atoms using a freeze group, and it would be easiest if I could do this from the get-go (i.e., without running equilibration in which the carbon atoms are unfrozen). Do you have any advice about which file format I should use? I need not be "constrained" by .gro (http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_ne ed_for_a_.gro_file). .pdb, it seems (http://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)#Example), gives position precision up to 0.001 ANGSTROM (or 0.0001 nm), which means .pdb will give me just enough precision. Or should I instead write my starting configuration in a .g96 file, which allows very high position precision? However, other than http://manual.gromacs.org/current/online/g96.html, I am having some difficulty (even with Google) locating detailed information about the .g96 file format. Unfortunately, my institution I do not think has a GROMOS-96 license, so I cannot access its manual. Between .pdb and .g96, which would you recommend? Or is there any other structure file format that I am not thinking of? Thanks so much. Andrew DeYoung Carnegie Mellon University -- 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] Amber99bsc0
Hi! I want to use amber99bsc0 in gromacs. is it possible? thanks. -- 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] Re: Gromacs-GPU benchmark test killed after exhausting the memory
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 >Subject: Re: [gmx-users] Gromacs-GPU benchmark test killed after >exhausting the memory >To: Discussion list for GROMACS users >Message-ID: > >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 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 runchkmem.out Description: runchkmem.out runchkmem_c.sh Description: runchkmem_c.sh -- 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 using OPLS forcefield parameter in lipid simulation
On 4/03/2012 10:15 PM, Anushree Tripathi wrote: I am not getting the "ffoplsaanb.itp" file for lipid simulation.PLease tell me how to locate the file. It depends on your system and GROMACS version. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation and pdb2gmx -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
[gmx-users] problem in using OPLS forcefield parameter in lipid simulation
I am not getting the "ffoplsaanb.itp" file for lipid simulation.PLease tell me how to locate the file. -- 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
