Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 Tsjerk On Oct 28, 2011 6:27 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Make su... I used the initial mdrun .tpr. After checking the generated pdb (total 51 frames), the first 28/29 frames both are together, but later are separated. (the intra_fit also not work as expected). So I think at beginning the reference initial ones are together. This .xtc were trjcat together, first 200ns and then extend to 500ns, the .pdb generated used dt 10ns. Cheers, Am I wrong in some places? Actually for other trajectories I had no problem (use the same way of handling it). Thanks, Tsjerk On Oct 27, 2011 11:47 AM, lina lina.lastn...@gmail.com wrote: Hi, I have ... -- 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 attachment: Screenshot-2.png-- 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] query on OPLS-2005
Hi Sanku According to the Schrodinger Knowledge Base, this is the paper that should be referenced for OPLS-2005 instead: Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts,T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky,L.Y. Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, and R.M. Levy. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comp. Chem., 26, 1752 (2005) (http://onlinelibrary.wiley.com/doi/10.1002/jcc.20292/full) The Gromacs oplsaa.ff/forcefield.doc file says OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) OPLS-AA/L seems to presented in the above paper as their updated version, but it is sourced from the 2001 paper on proteins which is listed as a reference in the Gromacs oplsaa.ff/forcefield.itp file. The 2005 paper then adds the following: New force-field parameters were developed for OPLS_2003 for organic functional groups for which the OPLS_2001 force field does not provide specific parameters. Previously derived parameters for proteins, discussed above, were implemented without modification in OPLS_2003. (Where 2003 apparently evolved into 2005). So it looks like the protein section of both force-fields are the same, but if you want to use other parameters you should check them individually first to see whether or not they were changed or created since 2001. Cara Date: Wed, 26 Oct 2011 15:02:07 -0700 From: msank...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] query on OPLS-2005 Hi, I wanted to check what is actually OPLS-2005 forcefield that is recently being referred often for md simulation. However, I also see that whenever, OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS forcefield. So, what is actually OPLS-2005?So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series. Is it also so-called OPLS-2005 forcefield?Sanku -- 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] trjconv and -pbc
Hi Lina, My previous reply was from before I looked at the graph. Have you considered that the molecule might be taking a stroll and turn back, or goes to another side of the protein? Have you looked at the trajectory, in particular at the trajectory with the jumps removed? Cheers, Tsjerk On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work. Cheers, Tsjerk On Oct 28, 2011 9:01 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 Tsjerk On Oct 28, 2011 6:27 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g... -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Parametrisation of the heteroatomic pdb
Dear Gromacs users! I've forced with some problem of preparing topology of my input pdb via pdb2gmx. My input structure( gramicidin ion chanell) consist of some heteroatoms due to the presence of the non standart aminoacids in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L analogs) I've tried to parametriesed that structure via different force fields but in all cases there are not suitable topologies for that aminoacids e.g Fatal error: Residue 'FOR' not found in residue topology database How I can solve that problem? I've tried to look for the suitable itp file but could not find it too :( 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] trjconv and -pbc
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, My previous reply was from before I looked at the graph. Have you considered that the molecule might be taking a stroll and turn back, Ha ... stroll?! or goes to another side of the protein? Have you looked at the trajectory, in particular at the trajectory with the jumps removed? I extracted the parts from 280ns to 300ns, the presentation of that part protein is not whole. In the former way, the time since 280ns till the end, the small molecular still outside the cell/box. even the minidist is very small later. I am not sure how to get the trajectory and view? (ngmx? ) Thanks, Cheers, Tsjerk On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work. Cheers, Tsjerk On Oct 28, 2011 9:01 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 Tsjerk On Oct 28, 2011 6:27 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g... -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] umbrella sampling
Hello, I am doing umbrella sampling to calculate PMF curve for the detachment of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5 ang, I did umbrella sampling on 25 configurations (for 5ns) and the window size is 0.5 ang. I used the following pulling code for umbrella sampling, pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 1000 pull_nstfout= 1000 I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM distance between the chain_A (terminal) and chain_B (2nd CP) should be restrained. after 5ns of umbrella sampling, I calculated the COM distance between chain A and B, but it was not restrained, for the 5.5 ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang. and also the pulling cyclic peptide undergoes large conformational sampling. from the WHAM analysis I understood the sampling window is poorly represented. In addition to COM distance restrain, can I restrain the pulling CP's backbone atoms? so that the pulling groups large conformational sampling will be reduced. I am using gromacs 4.5.5 version. Regards, Vijay. -- 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] Parametrisation of the heteroatomic pdb
James Starlight wrote: Dear Gromacs users! I've forced with some problem of preparing topology of my input pdb via pdb2gmx. My input structure( gramicidin ion chanell) consist of some heteroatoms due to the presence of the non standart aminoacids in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L analogs) I've tried to parametriesed that structure via different force fields but in all cases there are not suitable topologies for that aminoacids e.g Fatal error: Residue 'FOR' not found in residue topology database How I can solve that problem? I've tried to look for the suitable itp file but could not find it too :( For new protein residues, you do not need an .itp file, you need a suitable .rtp entry such that pdb2gmx can incorporate it into your topology. http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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
Vijayaraj wrote: Hello, I am doing umbrella sampling to calculate PMF curve for the detachment of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5 ang, I did umbrella sampling on 25 configurations (for 5ns) and the window size is 0.5 ang. I used the following pulling code for umbrella sampling, pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 1000 pull_nstfout= 1000 I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM distance between the chain_A (terminal) and chain_B (2nd CP) should be restrained. after 5ns of umbrella sampling, I calculated the COM distance between chain A and B, but it was not restrained, for the 5.5 ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang. and also the pulling cyclic peptide undergoes large conformational sampling. from the WHAM analysis I understood the sampling window is poorly represented. In addition to COM distance restrain, can I restrain the pulling CP's backbone atoms? so that the pulling groups large conformational sampling will be reduced. You could implement dihedral restraints to fix the backbone secondary structure, but I can't comment on the stability of trying to use these restraints in addition to the pull code. Seems like a lot going on at once, to me. Also consider the fact that 5 ns is an extremely short timeframe to gather meaningful data. Perhaps you just need more time in each window to equilibrate. At the shortest COM distance, your two molecules are still likely experiencing some interactions, and it may require a great deal of sampling in this window to converge the simulations. You haven't shown the rest of your .mdp file (always a good idea!), so we can only guess at whether or not your other settings should lead to a sensible result. -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] extending umbrella sampling runs
Hi, I want to extend the umbrella sampling runs and have used the below commands: 1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr 2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr #extending the runs: 3) tpbconv -s umbrella0.tpr -extend 15000 -o umbrella_20ns_0.tpr 4) mdrun -s umbrella_20ns_0.tpr -cpi 0.cpt -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0_20.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr When i run the above mdrun command (4) I get the below error message. As I use .xtc file for analysis, I have not written separate .trr output files for each window. By default it writes single traj.trr file for all my windows. I removed the traj.trr file and carried out the mdrun step and i stil get the error message with traj.trr. Please can i Know how do I get about extending this run. Error message: Output file appending has been requested, but some output files listed in the checkpoint file 0.cpt are not present or are named differently by the current program: output files present: 0.log pullx-umbrella0.xvg pullf-umbrella0.xvg 0.xtc 0.edr output files not present or named differently: traj.trr --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 2139 Fatal error: File appending requested, but only 5 of the 6 output files are present. Kind Regards, Chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Parametrisation of the heteroatomic pdb
Justin, hello! I've found that D and L-isomers must be topological identicaly so I've used topology of Leu and Val residues for Dle and Dva resp. I've added information about topology of that two residues to the .rtp .hdb of my force field as well as to the http://www.gromacs.org/Documentation/File_Formats/.rtp_File residuetypes.dathttp://www.gromacs.org/Documentation/File_Formats/residuetypes.dat Then I've succsesfull generated topology for gramicidin via pdb2gmx. I have only questions about two terminal CAP groups used in the Gramicidin It was FOR group on the C-end HETATM1 C FOR A 1A -3.690 -1.575 -2.801 1.00 0.00 C HETATM2 O FOR A 1A -3.774 -1.363 -1.586 1.00 0.00 O HETATM3 H FOR A 1A -4.305 -1.047 -3.545 1.00 0.00 H and the ETA group on the N-end HETATM 267 C1 ETA A 15A 5.148 -0.421 8.762 1.00 0.00 C HETATM 268 C2 ETA A 15A 3.657 -0.080 8.832 1.00 0.00 C HETATM 269 N ETA A 15A 2.813 -1.244 8.933 1.00 0.00 N HETATM 270 O ETA A 15A 5.921 0.752 8.985 1.00 0.00 O HETATM 271 1HN ETA A 15A 2.507 -1.491 9.845 1.00 0.00 H HETATM 272 HO ETA A 15A 5.736 1.339 8.244 1.00 0.00 H HETATM 273 1H1 ETA A 15A 5.410 -1.174 9.531 1.00 0.00 H HETATM 274 2H1 ETA A 15A 5.374 -0.849 7.759 1.00 0.00 H HETATM 275 1H2 ETA A 15A 3.383 0.525 7.938 1.00 0.00 H HETATM 276 2H2 ETA A 15A 3.492 0.565 9.718 1.00 0.00 I could not find good analogue for that groups in Amber force field so I've desided to deleate that groups temporary. Could you tell me how I can add possible Caps on the C and N terms of each chain of my molecule via pdb2gmx ? In one tutorial I've found the -term function for that but in my case system didnt suggest me to add new caps James 2011/10/28 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Dear Gromacs users! I've forced with some problem of preparing topology of my input pdb via pdb2gmx. My input structure( gramicidin ion chanell) consist of some heteroatoms due to the presence of the non standart aminoacids in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L analogs) I've tried to parametriesed that structure via different force fields but in all cases there are not suitable topologies for that aminoacids e.g Fatal error: Residue 'FOR' not found in residue topology database How I can solve that problem? I've tried to look for the suitable itp file but could not find it too :( For new protein residues, you do not need an .itp file, you need a suitable .rtp entry such that pdb2gmx can incorporate it into your topology. http://www.gromacs.org/**Documentation/How-tos/**Parameterizationhttp://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/**Documentation/How-tos/Adding_** a_Residue_to_a_Force_Fieldhttp://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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/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] Hbonds - Res - Ligand
Dear Gmx Users, I have compared average number of hbonds per time frame between my ligand and protein: 1) Using trajectory obtained straight after simulations: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.146 2) Using trajectory modified by trjconv according to the PBC workflow on www.gromcacs.org : g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.156 Does anyone know why this value changed and I obtained slightly different results? 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] Re: umbrella sampling
Hi Justin, Here is my complete code for umbrella sampling title = Umbrella pulling simulation define = -DPOSRES_2 integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns nstcomm = 10 nstxout = 5 ; every 100 ps nstvout = 5 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 constraint_algorithm= lincs constraints = all-bonds continuation= yes nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = Protein SOL tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 1000 pull_nstfout= 1000 I will do this umbrella sampling for 10ns, Do you think the COM distance can converge after long simulation time? ie back to the restraint position. Regards, Vijay. Vijayaraj wrote: Hello, I am doing umbrella sampling to calculate PMF curve for the detachment of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5 ang, I did umbrella sampling on 25 configurations (for 5ns) and the window size is 0.5 ang. I used the following pulling code for umbrella sampling, pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 1000 pull_nstfout= 1000 I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM distance between the chain_A (terminal) and chain_B (2nd CP) should be restrained. after 5ns of umbrella sampling, I calculated the COM distance between chain A and B, but it was not restrained, for the 5.5 ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang. and also the pulling cyclic peptide undergoes large conformational sampling. from the WHAM analysis I understood the sampling window is poorly represented. In addition to COM distance restrain, can I restrain the pulling CP's backbone atoms? so that the pulling groups large conformational sampling will be reduced. You could implement dihedral restraints to fix the backbone secondary structure, but I can't comment on the stability of trying to use these restraints in addition to the pull code. Seems like a lot going on at once, to me. Also consider the fact that 5 ns is an extremely short timeframe to gather meaningful data. Perhaps you just need more time in each window to equilibrate. At the shortest COM distance, your two molecules are still likely experiencing some interactions, and it may require a great deal of sampling in this window to converge the simulations. You haven't shown the rest of your .mdp file (always a good idea!), so we can only guess at whether or not your other settings should lead to a sensible result. -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] Re: Hbonds - Res - Ligand
With other residues is the same... and changes are bigger. Which trajectory in this case is reliable? My wsteps in trjconv involves: 1. First make your molecules whole if you want them whole (system). 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. 4. Remove jumps if you want to have them removed using the first frame 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step. 6. Put everything in some box. 7. Fit if desired and don't use any PBC related option afterwards. On Fri, Oct 28, 2011 at 2:28 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx Users, I have compared average number of hbonds per time frame between my ligand and protein: 1) Using trajectory obtained straight after simulations: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.146 2) Using trajectory modified by trjconv according to the PBC workflow on www.gromcacs.org : g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.156 Does anyone know why this value changed and I obtained slightly different results? 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] trjconv and -pbc
Hi Lina, You first remove the jumps from the trajectory. Then you can view that trajectory with ngmx or with VMD. You can also then extract the frames around the 'jump' and look at them. But if the molecule goes unstuck and then crosses the boundary to get stuck to the protein again, it would give exactly that result: Visually, the molecule seems close, goes away and apparently gets stuck somewhere floating nowhere. But the minimal distance to the protein would be really minimal then go through a maximum and go to the minimal level again. Cheers, Tsjerk On Fri, Oct 28, 2011 at 12:31 PM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, My previous reply was from before I looked at the graph. Have you considered that the molecule might be taking a stroll and turn back, Ha ... stroll?! or goes to another side of the protein? Have you looked at the trajectory, in particular at the trajectory with the jumps removed? I extracted the parts from 280ns to 300ns, the presentation of that part protein is not whole. In the former way, the time since 280ns till the end, the small molecular still outside the cell/box. even the minidist is very small later. I am not sure how to get the trajectory and view? (ngmx? ) Thanks, Cheers, Tsjerk On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work. Cheers, Tsjerk On Oct 28, 2011 9:01 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 Tsjerk On Oct 28, 2011 6:27 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g... -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] umbrella sampling
You need to evaluate convergence yourself for any simulation. I suggest doing the whole thing twice (or more) with different starting conformations. Also, look at the PMF from block averaging (generate one PMF from the 0-2 ns data, another from the 2-4 ns data, and so on) and see if there is a systematic drift with time. In my opinion, if you really want to converge to within 5 kcal/mol without using additional restraints as Justin mentioned, then you should be expecting to do 100 ns per umbrella, and probably 1000 ns per umbrella. -- Thus additional restraints are a very good idea. To see about using additional restraints, check out this paper: THE JOURNAL OF CHEMICAL PHYSICS 125, 084902 (2006) and this one: Journal of Chemical Theory and Computation 3(4):1231-1235 (2007). They are not US, but the idea is the same. Chris. -- original message -- Hi Justin, Here is my complete code for umbrella sampling title = Umbrella pulling simulation define = -DPOSRES_2 integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns nstcomm = 10 nstxout = 5 ; every 100 ps nstvout = 5 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 constraint_algorithm= lincs constraints = all-bonds continuation= yes nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = Protein SOL tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 1000 pull_nstfout= 1000 I will do this umbrella sampling for 10ns, Do you think the COM distance can converge after long simulation time? ie back to the restraint position. Regards, Vijay. [Hide Quoted Text] Vijayaraj wrote: Hello, I am doing umbrella sampling to calculate PMF curve for the detachment of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5 ang, I did umbrella sampling on 25 configurations (for 5ns) and the window size is 0.5 ang. I used the following pulling code for umbrella sampling, pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 1000 pull_nstfout= 1000 I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM distance between the chain_A (terminal) and chain_B (2nd CP) should be restrained. after 5ns of umbrella sampling, I calculated the COM distance between chain A and B, but it was not restrained, for the 5.5 ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang. and also the pulling cyclic peptide undergoes large conformational sampling. from the WHAM analysis I understood the sampling window is poorly represented. In addition to COM distance restrain, can I restrain the pulling CP's backbone atoms? so that the pulling groups large conformational sampling will be reduced. You could implement dihedral restraints to fix the backbone secondary structure, but I can't comment on the stability of trying to use these restraints in addition to the pull code. Seems like a lot going on at once, to me. Also consider the fact that 5 ns is an extremely short timeframe to gather meaningful data. Perhaps you just need more time in each window to equilibrate. At the shortest COM distance, your two molecules are still likely experiencing some interactions, and it may require a great deal of sampling in this window to converge the simulations. You haven't shown the rest of your .mdp file (always a good idea!), so we can only guess at whether or not your other settings should lead to a sensible result. -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
Re: [gmx-users] Parametrisation of the heteroatomic pdb
James Starlight wrote: Justin, hello! I've found that D and L-isomers must be topological identicaly so I've used topology of Leu and Val residues for Dle and Dva resp. I've added information about topology of that two residues to the .rtp .hdb of my force field as well as to the http://www.gromacs.org/Documentation/File_Formats/.rtp_Fileresiduetypes.dat http://www.gromacs.org/Documentation/File_Formats/residuetypes.dat Then I've succsesfull generated topology for gramicidin via pdb2gmx. I have only questions about two terminal CAP groups used in the Gramicidin It was FOR group on the C-end HETATM1 C FOR A 1A -3.690 -1.575 -2.801 1.00 0.00 C HETATM2 O FOR A 1A -3.774 -1.363 -1.586 1.00 0.00 O HETATM3 H FOR A 1A -4.305 -1.047 -3.545 1.00 0.00 H and the ETA group on the N-end HETATM 267 C1 ETA A 15A 5.148 -0.421 8.762 1.00 0.00 C HETATM 268 C2 ETA A 15A 3.657 -0.080 8.832 1.00 0.00 C HETATM 269 N ETA A 15A 2.813 -1.244 8.933 1.00 0.00 N HETATM 270 O ETA A 15A 5.921 0.752 8.985 1.00 0.00 O HETATM 271 1HN ETA A 15A 2.507 -1.491 9.845 1.00 0.00 H HETATM 272 HO ETA A 15A 5.736 1.339 8.244 1.00 0.00 H HETATM 273 1H1 ETA A 15A 5.410 -1.174 9.531 1.00 0.00 H HETATM 274 2H1 ETA A 15A 5.374 -0.849 7.759 1.00 0.00 H HETATM 275 1H2 ETA A 15A 3.383 0.525 7.938 1.00 0.00 H HETATM 276 2H2 ETA A 15A 3.492 0.565 9.718 1.00 0.00 I could not find good analogue for that groups in Amber force field so I've desided to deleate that groups temporary. Could you tell me how I can add possible Caps on the C and N terms of each chain of my molecule via pdb2gmx ? In one tutorial I've found the -term function for that but in my case system didnt suggest me to add new caps You have to build capping groups onto the termini. See, for instance the [ACE] and [NME] groups in the .rtp file. -Justin James 2011/10/28 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Dear Gromacs users! I've forced with some problem of preparing topology of my input pdb via pdb2gmx. My input structure( gramicidin ion chanell) consist of some heteroatoms due to the presence of the non standart aminoacids in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L analogs) I've tried to parametriesed that structure via different force fields but in all cases there are not suitable topologies for that aminoacids e.g Fatal error: Residue 'FOR' not found in residue topology database How I can solve that problem? I've tried to look for the suitable itp file but could not find it too :( For new protein residues, you do not need an .itp file, you need a suitable .rtp entry such that pdb2gmx can incorporate it into your topology. http://www.gromacs.org/__Documentation/How-tos/__Parameterization http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/__Documentation/How-tos/Adding___a_Residue_to_a_Force_Field http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-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 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 http://www.gromacs.org/Support/Mailing_Lists -- 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
[gmx-users] Re: Hbonds - Res - Ligand
Hi Justin, Do you have any clue of this problem? You are the last hope, please help :) Steven On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann s.neuman...@gmail.comwrote: With other residues is the same... and changes are bigger. Which trajectory in this case is reliable? My wsteps in trjconv involves: 1. First make your molecules whole if you want them whole (system). 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. 4. Remove jumps if you want to have them removed using the first frame 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step. 6. Put everything in some box. 7. Fit if desired and don't use any PBC related option afterwards. On Fri, Oct 28, 2011 at 2:28 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx Users, I have compared average number of hbonds per time frame between my ligand and protein: 1) Using trajectory obtained straight after simulations: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.146 2) Using trajectory modified by trjconv according to the PBC workflow on www.gromcacs.org : g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.156 Does anyone know why this value changed and I obtained slightly different results? 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] extending umbrella sampling runs
Hi, I want to extend the umbrella sampling runs and have used the below commands: 1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr 2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr #extending the runs: 3) tpbconv -s umbrella0.tpr -extend 15000 -o umbrella_20ns_0.tpr 4) mdrun -s umbrella_20ns_0.tpr -cpi 0.cpt -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0_20.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr When i run the above mdrun command (4) I get the below error message. As I use .xtc file for analysis, I have not written separate .trr output files for each window. By default it writes single traj.trr file for all my windows. I removed the traj.trr file and carried out the mdrun step and i stil get the error message with traj.trr. Please can i Know how do I get about extending this run. Error message: Output file appending has been requested, but some output files listed in the checkpoint file 0.cpt are not present or are named differently by the current program: output files present: 0.log pullx-umbrella0.xvg pullf-umbrella0.xvg 0.xtc 0.edr output files not present or named differently: traj.trr --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 2139 Fatal error: File appending requested, but only 5 of the 6 output files are present. Kind Regards, Chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] file.itp for separated molecules
Hello I have to question. 1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx. the pdb file contains 18 separate chains, in each chain, there are 6 residues. When I generate the topology and coordinates, it creates 18 posres-protein$i.itp file and 18 topol-protein$i.itp file and then one topol.top and one conf.gro ... is it normal? i think it is just the position restraint for separate chains ... in this way i think it enables me to restraint them separately if i want? right? 2- using topol.top and conf.gro, after solvating the molecule in the box of water ... with editconf and genbox ... I am trying to generate a tpr file, but when it generate it writes the following: Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'Protein2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 3 bonded neighbours molecule type 'Protein7' Excluding 3 bonded neighbours molecule type 'Protein8' Excluding 3 bonded neighbours molecule type 'Protein9' Excluding 3 bonded neighbours molecule type 'Protein10' Excluding 3 bonded neighbours molecule type 'Protein11' Excluding 3 bonded neighbours molecule type 'Protein12' Excluding 3 bonded neighbours molecule type 'Protein13' Excluding 3 bonded neighbours molecule type 'Protein14' Excluding 3 bonded neighbours molecule type 'Protein15' Excluding 3 bonded neighbours molecule type 'Protein16' Excluding 3 bonded neighbours molecule type 'Protein17' Excluding 3 bonded neighbours molecule type 'Protein18' Excluding 2 bonded neighbours molecule type 'SOL' what is this telling me? I didn't find a solution searching in the mailing list?! Thanks Fahimeh -- 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] Parametrisation of the heteroatomic pdb
I understood that but how I can add that groups to termi of the bowh of my chains ? I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS. May be Amber ff didnt support this feature ? James You have to build capping groups onto the termini. See, for instance the [ACE] and [NME] groups in the .rtp file. -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] query on OPLS-2005
Hi Cara, Thanks for a very clarifying email. It helps a lot. Sanku From: Cara Kreck cara_...@hotmail.com To: gmx-users@gromacs.org Sent: Friday, October 28, 2011 3:50 AM Subject: RE: [gmx-users] query on OPLS-2005 Hi Sanku According to the Schrodinger Knowledge Base, this is the paper that should be referenced for OPLS-2005 instead: Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts,T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky,L.Y. Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, and R.M. Levy. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comp. Chem., 26, 1752 (2005) (http://onlinelibrary.wiley.com/doi/10.1002/jcc.20292/full) The Gromacs oplsaa.ff/forcefield.doc file says OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) OPLS-AA/L seems to presented in the above paper as their updated version, but it is sourced from the 2001 paper on proteins which is listed as a reference in the Gromacs oplsaa.ff/forcefield.itp file. The 2005 paper then adds the following: New force-field parameters were developed for OPLS_2003 for organic functional groups for which the OPLS_2001 force field does not provide specific parameters. Previously derived parameters for proteins, discussed above, were implemented without modification in OPLS_2003. (Where 2003 apparently evolved into 2005). So it looks like the protein section of both force-fields are the same, but if you want to use other parameters you should check them individually first to see whether or not they were changed or created since 2001. Cara Date: Wed, 26 Oct 2011 15:02:07 -0700 From: msank...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] query on OPLS-2005 Hi, I wanted to check what is actually OPLS-2005 forcefield that is recently being referred often for md simulation. However, I also see that whenever, OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS forcefield. So, what is actually OPLS-2005? So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series. Is it also so-called OPLS-2005 forcefield? Sanku -- 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 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] lost ngmx
Hello gmx-users I have compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with ssh. Do I need to install gnome or kde? if the answer is yes, Do I need to compile gromacs again? or Is there a way to just compile ngmx? Thanks in advance -- Víctor E. Bahamonde Padilla Laboratorio Fisicoquimica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl -- 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] extending umbrella sampling runs
Poojari, Chetan wrote: Hi, I want to extend the umbrella sampling runs and have used the below commands: 1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr 2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr #extending the runs: 3) tpbconv -s umbrella0.tpr -extend 15000 -o umbrella_20ns_0.tpr 4) mdrun -s umbrella_20ns_0.tpr -cpi 0.cpt -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0_20.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr When i run the above mdrun command (4) I get the below error message. As I use .xtc file for analysis, I have not written separate .trr output files for each window. By default it writes single traj.trr file for all my windows. I removed the traj.trr file and carried out the mdrun step and i stil get the error message with traj.trr. Please can i Know how do I get about extending this run. Error message: Output file appending has been requested, but some output files listed in the checkpoint file 0.cpt are not present or are named differently by the current program: output files present: 0.log pullx-umbrella0.xvg pullf-umbrella0.xvg 0.xtc 0.edr output files not present or named differently: traj.trr --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 2139 Fatal error: File appending requested, but only 5 of the 6 output files are present. If you have overwritten or deleted the traj.trr file(s), you cannot append. Either use mdrun -noappend or run your jobs such that either (1) you use a unique filename for the .trr files or (2) you set nstxout=nstvout=nstfout=0 so that the .trr file is not written at all. -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: Hbonds - Res - Ligand
Steven Neumann wrote: Hi Justin, Do you have any clue of this problem? You are the last hope, please help :) Sorry, I have no idea. If I did, I would have posted earlier. In principle, PBC re-imaging should not affect the calculation of distances and angles needed by g_hbond and I have never seen such an outcome. -Justin Steven On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com wrote: With other residues is the same... and changes are bigger. Which trajectory in this case is reliable? My wsteps in trjconv involves: 1. First make your molecules whole if you want them whole (system). 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. 4. Remove jumps if you want to have them removed using the first frame 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. 6. Put everything in some box. 7. Fit if desired and don't use any PBC related option afterwards. On Fri, Oct 28, 2011 at 2:28 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com wrote: Dear Gmx Users, I have compared average number of hbonds per time frame between my ligand and protein: 1) Using trajectory obtained straight after simulations: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.146 2) Using trajectory modified by trjconv according to the PBC workflow on www.gromcacs.org http://www.gromcacs.org/ : g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.156 Does anyone know why this value changed and I obtained slightly different results? 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] file.itp for separated molecules
Fahimeh Baftizadeh wrote: Hello I have to question. 1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx. the pdb file contains 18 separate chains, in each chain, there are 6 residues. When I generate the topology and coordinates, it creates 18 posres-protein$i.itp file and 18 topol-protein$i.itp file and then one topol.top and one conf.gro ... is it normal? Yes, pdb2gmx will write topologies for whatever molecules it finds (and obviously has .rtp entries for). i think it is just the position restraint for separate chains ... in this way i think it enables me to restraint them separately if i want? right? Yes. 2- using topol.top and conf.gro, after solvating the molecule in the box of water ... with editconf and genbox ... I am trying to generate a tpr file, but when it generate it writes the following: Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'Protein2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 3 bonded neighbours molecule type 'Protein7' Excluding 3 bonded neighbours molecule type 'Protein8' Excluding 3 bonded neighbours molecule type 'Protein9' Excluding 3 bonded neighbours molecule type 'Protein10' Excluding 3 bonded neighbours molecule type 'Protein11' Excluding 3 bonded neighbours molecule type 'Protein12' Excluding 3 bonded neighbours molecule type 'Protein13' Excluding 3 bonded neighbours molecule type 'Protein14' Excluding 3 bonded neighbours molecule type 'Protein15' Excluding 3 bonded neighbours molecule type 'Protein16' Excluding 3 bonded neighbours molecule type 'Protein17' Excluding 3 bonded neighbours molecule type 'Protein18' Excluding 2 bonded neighbours molecule type 'SOL' what is this telling me? I didn't find a solution searching in the mailing list?! This is completely normal output. Please see the manual, section 5.4 and the footnotes of Table 5.4 for the specifics of the nrexcl value. -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] Parametrisation of the heteroatomic pdb
James Starlight wrote: I understood that but how I can add that groups to termi of the bowh of my chains ? I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS. May be Amber ff didnt support this feature ? pdb2gmx does not build things that aren't there. Your input coordinate file needs to have the capping groups present, with all atoms named as the .rtp entries expect them, hence the suggestion to investigate the [ACE] and [NME] directives. -Justin James You have to build capping groups onto the termini. See, for instance the [ACE] and [NME] groups in the .rtp file. -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] Parametrisation of the heteroatomic pdb
Justin? So As I understood the aminoacids.rtp of current force field must include topology for such caps. But for example If I have only topology on such groups for another ff could I include it to the amber FF? If no where I could find such topology ? James 2011/10/28 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: I understood that but how I can add that groups to termi of the bowh of my chains ? I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS. May be Amber ff didnt support this feature ? pdb2gmx does not build things that aren't there. Your input coordinate file needs to have the capping groups present, with all atoms named as the .rtp entries expect them, hence the suggestion to investigate the [ACE] and [NME] directives. -Justin James You have to build capping groups onto the termini. See, for instance the [ACE] and [NME] groups in the .rtp file. -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/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
Re: [gmx-users] Parametrisation of the heteroatomic pdb
James Starlight wrote: Justin? So As I understood the aminoacids.rtp of current force field must include topology for such caps. Yes. Any residue whatsoever that you wish to process with pdb2gmx must be present in an .rtp file. But for example If I have only topology on such groups for another ff could I include it to the amber FF? If no where I could find such topology ? Do not mix and match force fields. Even if you can hack it into working, the results will be absolute garbage. If you need a topology for a specific force field, refer to the parameterization link I posted before. Deriving parameters for new residues in an existing force field is a task that may take weeks or months to do properly and hence is considered an expert topic. I have nothing more to contribute on that issue. The archives are filled with tips and discussions on how to go about such things. -Justin James 2011/10/28 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: I understood that but how I can add that groups to termi of the bowh of my chains ? I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS. May be Amber ff didnt support this feature ? pdb2gmx does not build things that aren't there. Your input coordinate file needs to have the capping groups present, with all atoms named as the .rtp entries expect them, hence the suggestion to investigate the [ACE] and [NME] directives. -Justin James You have to build capping groups onto the termini. See, for instance the [ACE] and [NME] groups in the .rtp file. -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 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-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 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 http://www.gromacs.org/Support/Mailing_Lists -- 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] pdb2gmx problem with ACE N-cap
Hi, I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I get following error message: Program pdb2gmx_44, VERSION 4.5.4 Source code file: pdb2top.c, line: 1070 Fatal error: atom N not found in buiding block 1ACE while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I wonder how I can make sure that ACE can be used as N-terminus. Sanku-- 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 problem with ACE N-cap
Sanku M wrote: Hi, I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I get following error message: Program pdb2gmx_44, VERSION 4.5.4 Source code file: pdb2top.c, line: 1070 Fatal error: atom N not found in buiding block 1ACE while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I wonder how I can make sure that ACE can be used as N-terminus. You've somehow constructed the cap wrong. There is no N atom in ACE. Check the .rtp for what's required, check your coordinate file, and make sure you're using -ter none with pdb2gmx. If that's still not working, post your command and relevant snippet of your coordinate file. -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] How to change moment of inertia of a molecule
Dear Gromacs Users, I want to run a calculation using Gromacs for some mixed/water solutions by changing moment of inertia of molecules. Can anyone please tell me is there any one of changing the actual moment of inertia of a molecule e.g. water Any comments will be really appreciated. Thanks and Regards, Rini Gupta UBC, Vancouver -- 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 change moment of inertia of a molecule
On 29/10/2011 9:04 AM, Rini Gupta wrote: Dear Gromacs Users, I want to run a calculation using Gromacs for some mixed/water solutions by changing moment of inertia of molecules. Can anyone please tell me is there any one of changing the actual moment of inertia of a molecule e.g. water You will need to change the mass of the atom(s) and that requires creating a new atom type with the mass you want, and a new molecule type for each such modified molecule that refers to the new atom type. 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] lost ngmx
On 29/10/2011 3:51 AM, Victor wrote: Hello gmx-users I have compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with ssh. You probably need more than the Xorg executables to compile ngmx, but I can't suggest what other than both X libraries and header files (e.g. devel packages). Do I need to install gnome or kde? No. if the answer is yes, Do I need to compile gromacs again? or Is there a way to just compile ngmx? No. 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
