Re: [gmx-users] Lie method for binding free energy calculations
Hi, You can email me we have a tool for mmpbsa with gromacs Andrea Messaggio inviato dal mio ASUS MeMO Pad Justin Lemkul jalem...@vt.edu ha scritto: On 10/25/13 11:43 AM, Sajad Ahrari wrote: is AMBER facilities the only way of approaching MM-PBSA calculations? could you lead me to any other software more friendly with Gromacs MD output? See what Google tells you. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] nstcalclr bug?
Hi there, I am using gromacs-4.6.1 with this mdp file: integrator = md; leap-frog integrator nsteps = 300 ; 6.0 ns dt = 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 5 ps nstcalcenergy = 100 ; nstxtcout = 5000 ; xtc every 10 ps xtc_precision = 100 continuation= yes ; Restarting constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 20; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) nstcalclr= 10 cutoff-scheme = Group vdwtype = Cut-off vdw-modifier = Potential-shift coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT coulomb-modifier = Potential-shift tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K energygrps = complex Water; group(s) to write to energy file pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com pbc = xyz ; 3-D PBC DispCorr= EnerPres ; account for cut-off vdW scheme gen_vel = no; Velocity generation is off gen-seed= 128742 ; number of steps for center of mass motion removal nstcomm = 1000 the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says nstcalclr = 0. If I set rvdw = 1.4 ( rlist), gmxdump of the file tpr is now correct to nstcalclr = 10. I have double checked the manual but I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- 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] OPLS-AA parameters for Phospho-threonine and serine
Hi, Have look here: http://haddock.science.uu.nl/services/HADDOCK/library.html The ff used by HADDOCK is oplsx derived from opls. Maybe you can exploit them as starting point. Hope it helps And Martin, Erik W erik.mar...@stjude.org ha scritto: I've searched the literature and internet and can't seem to find anything. I need to rerun some simulations I've run previously with OPLS-AA (and eventually gromos 54A7 when I'm done with OPLS) and need to include phosphorylated residues. I'm parameterized residues in Amber and Charmm, so I'm willing to do it here if required… but would be shocked if nobody has done this before. Are the parameters for these residues available somewhere. Thanks for the help, Erik Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer -- 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
R: [gmx-users] metadynamics
Hi, have look to: http://www.plumed-code.org/ and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics Basilica San Raffaele, 3P 34R Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ www.biomolnmr.org Tel: 0039-0226434348 Fax: 0039-0226434153 -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 07636600962 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di Sathish Kumar [sathishk...@gmail.com] Inviato: sabato 18 maggio 2013 12.26 A: Discussion list for GROMACS users Oggetto: [gmx-users] metadynamics Sir, i want to learn about metadynamics, how to run metadynamics in gromacs.please suggest me in this regard. Thank you. -- regards M.SathishKumar -- 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] different checkpoint from remd after crash
Hi there, I am performing a remd (8 replica) using gromacs-4.5.3 Unfortunately, the job crashed for a problem with our cluster. We attempted to restart the simulation using the checkpoint files, but two on the eight have different time frame. To restart the simulation, I used the old feature of tpbconv, i.e. cut the all trr files to the same time, regenerate new tpr files from them. I am wondering whether there is a smart way to proceed in that situation, i.e. generate a new checkpoint file from the trr. thanks in advance and -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://biomolnmr.org/ http://www.linkedin.com/in/andreaspitaleri - -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 07636600962 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.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] different checkpoint from remd after crash
Hi, unfortunately state_prev.cpt are different too (checked with gmxcheck). So, the only way to restart is the old fashion? thanks and On 04/19/2013 04:13 PM, Mark Abraham wrote: This is part of what state_prev.cpt is for - if only some of the new .cpt files have made it to disk, you still have a full set of matching .cpt files, but not with consistent names. Use gmxcheck to see the times. Mark On Fri, Apr 19, 2013 at 3:24 PM, andrea spitaleri spitaleri.and...@hsr.itwrote: Hi there, I am performing a remd (8 replica) using gromacs-4.5.3 Unfortunately, the job crashed for a problem with our cluster. We attempted to restart the simulation using the checkpoint files, but two on the eight have different time frame. To restart the simulation, I used the old feature of tpbconv, i.e. cut the all trr files to the same time, regenerate new tpr files from them. I am wondering whether there is a smart way to proceed in that situation, i.e. generate a new checkpoint file from the trr. thanks in advance and -- --**--**- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/**andreaspitaleri/http://sites.google.com/site/andreaspitaleri/ http://biomolnmr.org/ http://www.linkedin.com/in/**andreaspitalerihttp://www.linkedin.com/in/andreaspitaleri --**--**- --**--** -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 07636600962 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -- 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 -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://biomolnmr.org/ http://www.linkedin.com/in/andreaspitaleri - -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 07636600962 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.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
R: [gmx-users] Metadynamics with Esential Dynamics Sampling
Hi, I suggest you to visit the plumed webpage and ask to the mailing list. http://www.plumed-code.org/ best and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics Basilica San Raffaele, 3P 34R Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ www.biomolnmr.org Tel: 0039-0226434348 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di James Starlight [jmsstarli...@gmail.com] Inviato: venerdì 21 dicembre 2012 21.09 A: Discussion list for GROMACS users Oggetto: [gmx-users] Metadynamics with Esential Dynamics Sampling Dear Gromacs Users! Recently I've found algorithm for calculation of the free-energy along essential subspaces proposed by Spiwok. I wounder to know more about technical details of that algorithm. Earlier I've used Essential Dynamics sampling for simulation of membrane receptors. In that case I've created run edi files as well as run my simulations with Gromacs 4.5.5 on 100 nodes cluster. Has your algorithm compatibility with that Gromacs version ? Must I patch gromacs run files on both work-station ( where system preparation as well as generation of edi files are performed) as well as on cluster (where calculation via md_run) are performed ? Also I've found another possibility of using metadynamics in GROMACS ( e.g PLUMED). Have anybody try to use it? Did it compatible with the EDS ? Thanks for help, 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 -- 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] MM-GB/SA analysis in Gromacs
Dear all, I would like to bring to your attention this paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 in which we made a tool to perform MM/PBSA binding free energy calculation in automatic fashion, using torque/pbs parallel system implemented in most clusters. The input of the tools are just the xtc trajectory, the tpr and eventually the index file. It does perform the computational alanine scanning (CAS) too. The tool is available upon request. Further details on the paper. Regards, and On 11/29/2012 10:42 AM, Anna Marabotti wrote: Dear gmx-users, I ran several MD simulations using Gromacs 4.5.4 version, and now I'd need to calculate binding free energies using the MM-GBSA method. I searched through the manual and through the gmx-users archive, but I didn't find a way to do it. I found an old post in which it appeared that in the version 4.5 this possibility would have been available (http://lists.gromacs.org/pipermail/gmx-users/2010-July/052302.html), but it seems to me that this kind of analysis has not been implemented yet. In another more recent post, I see that somebody has used mdrun -rerun in order to perform calculations, but I don't understand the correct procedure to use (apart from the suggestion of using .trr instead of .xtc files in order to avoid errors). Does anyone have suggestions in order to do this analysis with Gromacs trajectories, before I make these calculations with another program? Many thanks in advance and best regards Anna -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- 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] force vs time plot
Hi to all gromacs users, I am trying to run an umbrella sampling and i am getting the initial conformations by pulling simulations but i want to check the simulation through the force vs time plot to see if my complex did or did not separate, so how can i get this plot? Thank you for your time Paula -- 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] vacuum simulation problem with pdb file
Hi all, I am trying to do a vacuum simulation with distance restrain, first i did an EM without distance restrastraints, later i did 100 ps to stabilized the T at 300 K but i get this in the pdb file ATOM 1 N MET 1 nan nan nan 1.00 0.00 ATOM 2 H1 MET 1 nan nan nan 1.00 0.00 ATOM 3 H2 MET 1 nan nan nan 1.00 0.00 ATOM 4 CA MET 1 nan nan nan 1.00 0.00 ATOM 5 CB MET 1 nan nan nan 1.00 0.00 ATOM 6 CG MET 1 nan nan nan 1.00 0.00 ATOM 7 SD MET 1 nan nan nan 1.00 0.00 ATOM 8 CE MET 1 nan nan nan 1.00 0.00 ATOM 9 C MET 1 nan nan nan 1.00 0.00 ATOM 10 O MET 1 nan nan nan 1.00 0.00 ATOM 11 N THR 2 nan nan nan 1.00 0.00 ATOM 12 H THR 2 nan nan nan 1.00 0.00 ATOM 13 CA THR 2 nan nan nan 1.00 0.00 ATOM 14 CB THR 2 nan nan nan 1.00 0.00 ATOM 15 OG1 THR 2 nan nan nan 1.00 0.00 ATOM 16 HG1 THR 2 nan nan nan 1.00 0.00 ATOM 17 CG2 THR 2 nan nan nan 1.00 0.00 Besides it creates several pdb files call step#b_n#.pdb that seems to contain coordinates of some atoms in each file. Thanks for your help Paula -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] distance restraint
Hello gromacs users, I am doing energy minimization of a big protein with distance restraint (i need to create interactions between a group of residues, so i need them to be close), but in the resultant pdb a don't see those residues close, so how can I verify that the distance restraint are working?. Another unrelated question, is that i am doing the simulation in vacumm, also in this case i need to neutralized the system?, because with the command genion i need solvent to replace by ions, so in this case i can't do that part. Thanks for your help Paula -- 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
Good morning, I am trying to run an umbrella sampling simulation, my system is a complex of two proteins. I have a couple of questions: 1. i don't know which is the purpose in defining the charge of each protein end 2. When i check the topol.itp file of the reference molecule i realized that it already has #ifdef POSRES_B #include posre_B.itp #endif and when i check the file of the other protein it has it too 3. I don't know how to decide the size of the unit cell and which is the criterion to center the molecules 4. I am not sure why in the equilibration step and NVT it hasn't been done 5. In the neutralization part in this kind of simulation ones has to specified the concentration of the solution or i can do it just with the number of ions i want to add Thank you Paula -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] fixing split molecules in trajectory file
Good afternoon, I run a molecular dynamics simulation of two protein complex with periodic boundaries, when i check the trajectory file i realized that the molecules were split so i decided to use the trjconv command with the option -pbc, i tried with -pbc atom, -pbc res and they didn't seem to work or i am not very sure what they do, but whet i used -pbc whole i achieved complete molecules but they are supposed to be in contact but it seem that this option (whole), besides fixing the problem of split molecules they put the in different positions (before i run trjconv the complex was bind, after the proteins are unbound). Another question is that after MD simulation i calculate distances between the two proteins along through with the command g_dist, i want to know if this calculation is correct even if don't fix the trajectory Thank you for your time Paula -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] force field parametrs for Mn2+
Hi, we published recently a paper where we determined the oplsaa parameters for Mn2+; have look to (supp mat): http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract hope it helps On 07/09/2012 12:21 PM, tarak karmakar wrote: Dear All, Please suggest me any paper/article that contains force field parameters for Mn 2+ . Thanks -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] hydration layers around protein
One option is to calculate the rdf (radial distribution function g_rdf [-surf]) of water oxygen atoms and find the position of the first few peaks... Il 29/05/2012 12:28, Bala subramanian ha scritto: Friends, I read in many articles explaining the behaviour of water in the first (or second etc) hydration layers around a protein. I am curious to know if there is any way to obtain/guess the thickness of this layer. How does one defines the thickness ? Thanks, Bala -- C. Balasubramanian -- *** Andrea Coletta - PhD Dip.to di Biologia - Stanza 326 Facoltà di Scienze - Università degli Studi di Roma Tor Vergata Via della Ricerca Scientifica snc, 00133, Roma, Italia Tel. +390672594326 Fax +39062022798 E-Mail: andrea.coletta_at_uniroma2_dot_it *** -- 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] PLUMED plugin in gromacs for protein system
Hi Neeru, this is an issue for the plumed mailing list. Try there. http://sites.google.com/site/plumedweb/home regards and On 04/19/2012 07:16 AM, neeru sharma wrote: Dear gromacs users, I am a gromacs user and need some help regarding the implementation of PLUMED plugin in gromacs. I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using Gromacs which is a 166 residue protein+mg+GTP/GDP complex. I have already carried out classical MD simulation for the Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now have to analyse the structural changes in the Protein-Mg-GTP complex during the simulation. I tried to perform classical MD simulation for the Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a millisecond time-scale event, through classical MD, it seems practically impossible to achieve this time-scale transition. I was looking for the methods available in gromacs that can accelerate this event. I came across the PLUMED plugin. I have some queries with respect to the above matter. 1) Can we manually specify simulation length when performing the simulation, that we want to finish the simulation in the given specified time duration? 2) How can we specify reaction coordinates (Eg: The RMSD with the desired output state, Specific H-bonding or distance pattern etc) for the simulation, as I already have the crystal structure available with me for the Protein-Mg-GTP complex (output state desired to be achieved with the simulation). As, I am new to gromacs, can you please help me regarding the above mentioned matter, usage of plumed plugin for protein system and how it can be approached with my system? Any help will be highly appreciated. Thanks in advance Regards, Neeru -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.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
[gmx-users] pdb2gmx -ter with cyclic peptide
Hi there, normally to generate a cyclic peptide I use to edit specbond.dat to force the bond between the N- and C-termini and I use the -ter flag into pdb2gmx tool in order to avoid to add hydrogens and oxygen to the end of the peptide. This was okay until the gromacs version 4.0.5 with opls ff. Now using gromacs 4.5.3 with opls ff I get this message: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. did something change or is is a bug? I have checked in the mailing list and I did not find any answer. thanks in advance for any help and -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- 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] angle between two domains connected at a hinge
Hi, have look to the orient package for vmd: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/ In the vmd script repository there is also a python script: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/fit_angle/ I have done a script using orient which calculate the angle between the principal axes of two selections. It is very rough but is does what you are asking. if you need it contact me and On 07/15/2011 03:37 PM, maria goranovic wrote: There must be several tools to calculate the angle between two domains connected at a hinge. I was wondering if someone has suggestions on any tools, or whether it is possible to do this using a vmd plugin directly for a trajectory? IN my case, I have a reasonable good idea where the hinge is. I was wondering if the angle between the principal axes of the domains would be good enough? For example, if the domains were two discs attached to a common hinge, how can I find the vector from the hinge in the direction of each disc?� � --� Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - - Dai il tuo 5XMILLE al San Raffaele. Basta una firma. Se firmi per la ricerca sanitaria del San Raffaele di Milano, firmi per tutti. C.F. 03 06 42 80 153. INFO: 5xmi...@hsr.it - www.5xmille.org -- 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] gnuplot
� -242128.531250 �� 95.40� -241968.015625 �� 95.60� -242318.781250 �� 95.80� -242614.875000 �� 96.00� -243034.734375 �� 96.20� -243061.171875 �� 96.40� -242386.781250 �� 96.60� -242364.687500 �� 96.80� -241825.093750 �� 97.00� -242219.50 �� 97.20� -242616.296875 �� 97.40� -242946.593750 �� 97.60� -242282.437500 �� 97.80� -242090.421875 �� 98.00� -241557.671875 �� 98.20� -242052.671875 �� 98.40� -242357.828125 �� 98.60� -242622.953125 �� 98.80� -242419.546875 �� 99.00� -242963.156250 �� 99.20� -242370.125000 �� 99.40� -242272.656250 �� 99.60� -242551.593750 �� 99.80� -242698.00 � 100.00� -242706.312500 -- Manoj Kumar Gadhwal (M. Pharma), Research Schloar, Prin. K. M. Kundnani College of Pharmacy, Colaba, Mumbai-05. Cont. No. +91 9769051866 -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - - Dai il tuo 5XMILLE al San Raffaele. Basta una firma. Se firmi per la ricerca sanitaria del San Raffaele di Milano, firmi per tutti. C.F. 03 06 42 80 153. INFO: 5xmi...@hsr.it - www.5xmille.org -- 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] xvg plotting
Hi there, in gnuplot you can do: gnuplotset datafile commentschars #% gnuplotfile(i) = sprintf(fio%d.xvg,i) gnuplotplot for[i=1:6] file(i) u 1:2 w lp in order to plot fio1.xvg fio2.xvg fio3.xvg fio4.xvg fio5.xvg fio6.xvg hope it helps and On 06/22/2011 01:38 AM, Dallas Warren wrote: Any graphing program will do, the .xvg file is a text data file, so you can import it into Excel, Sigma Plot, xmgrace, gnuplot etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:*gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Nicole Varvarigou *Sent:* Tuesday, 21 June 2011 7:40 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] xvg plotting Hi, I am a new user in gromacs and i would like to create a plot from several .xvg files. Can anyone guide me through the process? Thank you in advance N.V. -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - - Dai il tuo 5XMILLE al San Raffaele. Basta una firma. Se firmi per la ricerca sanitaria del San Raffaele di Milano, firmi per tutti. C.F. 03 06 42 80 153. INFO: 5xmi...@hsr.it - www.5xmille.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsdist error hi (-1000.000000) = lo (0.000000)
Hi all, I'm trying to use this tool with the following command (selecting the backbone atoms: 366 atoms in total) g_rmsdist -s 1.pdb -f traj_fit.trr -rms But the programs stop with the following error: Program g_rmsdist, VERSION 4.5.4 Source code file: matio.c, line: 953 Fatal error: hi (-1000.00) = lo (0.00) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Could you please help me? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://gryphus.chimfarm.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar -- 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] Error during PUMED installation for GROMACS-4.5.3
: cannot touch `./src/kernel//.deps/restraint_alfabeta.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_alpharmsd.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_angle.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_antibetarmsd.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_coord.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_dihcor.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_dipole.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_dist.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_elstpot.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_energy.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_hbonds.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_helix.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_mindist.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_parabetarmsd.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_position.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_puckering.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_rgyr.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_rmsdtor.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_spath.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_torsion.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_waterbridge.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/*.Po': No such file or directory - DONE! -- / - Thanks and regards /Bipin Singh/ / / / -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] xtc corrupted during REMD
Hi, two on five have magic error at the same time. The simulation ends fine. Just the xtc files are corrupted. The magic error is systematic, since I repeated the simulation 4 times and I get the same behavior (at different time) after the continuing run. First time, I suspected for some I/O error, but now it sounds a bit strange. I will ask for a long simulation 50ns without extending steps. thanks in advance regards and On 11/22/2010 05:44 AM, Roland Schulz wrote: On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea spitaleri.and...@hsr.it mailto:spitaleri.and...@hsr.it wrote: Hi, yes sure. Basically I do: 1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 - i get the first 5x25ns of remd simulation (five xtc every 5ps and five trr every 20ps, for each replica). I check those files by gmxcheck and they are fine. no errors. 2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 2500 -o runB_$i - extension the simulation to 50ns total 3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_ - at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted (from gmxcheck) whereas the trr are fine. These are from 25ns to 50ns. From the log file I do not see any errors. Everything seems fine. I have free room space in the hd too :) I am just wondering whether the problem is in the xtc options (precision and writing step) I doubt it that it has anything to do with your xtc options. Are all you xtc corrupted or only some? Are those which are corrupted all corrupted on the same frame or different ones? Roland Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] per conto di Mark Abraham [mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au] Inviato: domenica 21 novembre 2010 17.03 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] xtc corrupted during REMD On 21/11/2010 2:34 AM, Spitaleri Andrea wrote: Hi there, I am encountering a weird problem with a REMD simulation using 4.5.3. The total simulation is 50ns with 5 replica, and I do in two runs: 25ns and then continuing to 50ns (walltime queue). The first run is okay, the continue run (the last 25ns) randomly make some xtc files corrupted (from gmxcheck I get the Magic Number Error). I don't understand how the simulation can continue writing the .xtc files when you are getting magic number errors from gmxcheck. We need to see command lines for your workflow, please :-) Mark It is strange since the respective trr files are okay and the simulation is still going (it is not blowing up from the log, not step.pdb files, not crash). The only difference is that I am writing the xtc often respect to the trr file and just the complex not the solvent: nstxout = 1 ; coordinates every 20ps nstvout = 0 ; velocity every 0ps nstfout = 0 ; forces every 0 ps nstlog = 2500 ; energies log every 5ps nstenergy = 2500 ; energies every 5ps nstxtcout = 2500 ; coordinates every 5ps to xtc xtc-precision = 2500 ; xtc-grps= complex; Since the error is happening only for the continuing run, I am just wondering if there is any reason for this. thanks for any help and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org http://www.sanraffaele.org -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx
R: [gmx-users] xtc corrupted during REMD
Hi, yes sure. Basically I do: 1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 - i get the first 5x25ns of remd simulation (five xtc every 5ps and five trr every 20ps, for each replica). I check those files by gmxcheck and they are fine. no errors. 2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 2500 -o runB_$i - extension the simulation to 50ns total 3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_ - at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted (from gmxcheck) whereas the trr are fine. These are from 25ns to 50ns. From the log file I do not see any errors. Everything seems fine. I have free room space in the hd too :) I am just wondering whether the problem is in the xtc options (precision and writing step) thanks a lot and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di Mark Abraham [mark.abra...@anu.edu.au] Inviato: domenica 21 novembre 2010 17.03 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] xtc corrupted during REMD On 21/11/2010 2:34 AM, Spitaleri Andrea wrote: Hi there, I am encountering a weird problem with a REMD simulation using 4.5.3. The total simulation is 50ns with 5 replica, and I do in two runs: 25ns and then continuing to 50ns (walltime queue). The first run is okay, the continue run (the last 25ns) randomly make some xtc files corrupted (from gmxcheck I get the Magic Number Error). I don't understand how the simulation can continue writing the .xtc files when you are getting magic number errors from gmxcheck. We need to see command lines for your workflow, please :-) Mark It is strange since the respective trr files are okay and the simulation is still going (it is not blowing up from the log, not step.pdb files, not crash). The only difference is that I am writing the xtc often respect to the trr file and just the complex not the solvent: nstxout = 1 ; coordinates every 20ps nstvout = 0 ; velocity every 0ps nstfout = 0 ; forces every 0 ps nstlog = 2500 ; energies log every 5ps nstenergy = 2500 ; energies every 5ps nstxtcout = 2500 ; coordinates every 5ps to xtc xtc-precision = 2500 ; xtc-grps= complex; Since the error is happening only for the continuing run, I am just wondering if there is any reason for this. thanks for any help and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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] xtc corrupted during REMD
Hi there, I am encountering a weird problem with a REMD simulation using 4.5.3. The total simulation is 50ns with 5 replica, and I do in two runs: 25ns and then continuing to 50ns (walltime queue). The first run is okay, the continue run (the last 25ns) randomly make some xtc files corrupted (from gmxcheck I get the Magic Number Error). It is strange since the respective trr files are okay and the simulation is still going (it is not blowing up from the log, not step.pdb files, not crash). The only difference is that I am writing the xtc often respect to the trr file and just the complex not the solvent: nstxout = 1 ; coordinates every 20ps nstvout = 0 ; velocity every 0ps nstfout = 0 ; forces every 0 ps nstlog = 2500 ; energies log every 5ps nstenergy = 2500 ; energies every 5ps nstxtcout = 2500 ; coordinates every 5ps to xtc xtc-precision = 2500 ; xtc-grps= complex; Since the error is happening only for the continuing run, I am just wondering if there is any reason for this. thanks for any help and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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] remd with disre in gmx4.0.7
--- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C’E' CURA, SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 – www.sanraffaele.org---BeginMessage--- Hi there, this is a very old issue for me at lest and I still get error running a remd simulation using restraints for ion. I am using gmx4.0.7 This is my input: ; Distance restraints disre = simple disre_weighting = equal disre_fc= 1000 and in topol.top [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 957 309 1 01 0.18 0.20 0.25 1 957 338 1 11 0.18 0.20 0.25 1 957 701 1 21 0.18 0.20 0.25 1 957 733 1 31 0.18 0.20 0.25 1 956 149 1 41 0.18 0.20 0.25 1 956 185 1 51 0.18 0.20 0.25 1 956 417 1 61 0.18 0.20 0.25 1 956 462 1 71 0.18 0.20 0.25 1 So all different restraints. My input run is: #PBS -l nodes=120 mpirun mdrun_d -s remd -v -deffnm remd -multi 5 -replex 5000 -npme 8 -dd 4 4 1 and immediately I get: Program mdrun_d, VERSION 4.0.7 Source code file: disre.c, line: 143 Fatal error: Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd) That's strange since I am not neither using time nor ensemble averages nor multiple dist restraints. thansk in advance for any help and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di XAvier Periole [x.peri...@rug.nl] Inviato: giovedì 14 ottobre 2010 1.30 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] Martini parameters for monoolein I do not know what is the structure of monoolein :(( Then it is strongly possible that OH-C-C-OH is best represented by the P4 particle type. But it might not be that simple :)) you should once your (first) topology made try it out and compare to as much data you can find ... experimental and from atomistic simulations ... that should include dynamics, structure et thermodynamics ... have fun, XAvier. On Oct 13, 2010, at 2:06 PM, George Khelashvili wrote: Dear Xavier, I think I have figured out how to deal with the missing part. My problem was OH-C-C-OH construct which is the headgroup of monoolein. After some research, it looks like that it is parameterized based on ethanediol and has P4 type. The rest of the molecule I guess should be straightforward CG backbone plus CG tail beads. Can you comment on this? Thank you, George On 10/13/2010 3:56 PM, XAvier Periole wrote: Have you considered reading the few papers describing the principle of parameterization with the Martini FF? There are basic recipes described and specific applications detailed. Looking at cgmartini.nl might also help you getting more information and reach people involved in Martini parameterization :)) XAvier. On Oct 13, 2010, at 11:42 AM, George Khelashvili wrote: Dear users, I am trying to build Martini topology for monoolein molecule (I assume that no such topology exists at this moment). It is obvious that the tail part of the molecule is similar to DOPC lipid tail, however I am not sure how to parametrize the head-group of monoolein. I would appreciate if somebody could provide a guidance on this matter. Thank you, George -- 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 -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA gek2...@med.cornell.edu Phone: 1-212-746-6539 Fax: 1-212-746-6226 -- 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
R: [gmx-users] remd with disre in gmx4.0.7
--- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C’E' CURA, SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 – www.sanraffaele.org---BeginMessage--- Hi there, thanks for that. It makes clear. Regards and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di Mark Abraham [mark.abra...@anu.edu.au] Inviato: giovedì 14 ottobre 2010 3.16 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] remd with disre in gmx4.0.7 On 14/10/2010 12:09 PM, Justin A. Lemkul wrote: Spitaleri Andrea wrote: http://www.sanraffaele.org/grazieate Hi there, this is a very old issue for me at lest and I still get error running a remd simulation using restraints for ion. I am using gmx4.0.7 This is my input: ; Distance restraints disre = simple disre_weighting = equal disre_fc= 1000 and in topol.top [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 957 309 1 01 0.18 0.20 0.25 1 957 338 1 11 0.18 0.20 0.25 1 957 701 1 21 0.18 0.20 0.25 1 957 733 1 31 0.18 0.20 0.25 1 956 149 1 41 0.18 0.20 0.25 1 956 185 1 51 0.18 0.20 0.25 1 956 417 1 61 0.18 0.20 0.25 1 956 462 1 71 0.18 0.20 0.25 1 So all different restraints. My input run is: #PBS -l nodes=120 mpirun mdrun_d -s remd -v -deffnm remd -multi 5 -replex 5000 -npme 8 -dd 4 4 1 and immediately I get: Program mdrun_d, VERSION 4.0.7 Source code file: disre.c, line: 143 Fatal error: Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd) That's strange since I am not neither using time nor ensemble averages nor multiple dist restraints. You are using ensemble averaging, which is invoked when combining disre = simple and mdrun -multi, per the manual. You should be able to use mdrun -pd, as the error message suggests. That is, disre = simple and mdrun -multi combine to implement ensemble averaging. This seems not to be what the OP wanted, which seemed to be distance restraints with REMD. Other than using PD, there's no work-around in 4.0.x or current code. 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 ---End Message--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
R: [gmx-users] Conformational sampling
Dear Nisha, have look to the plumed plugin in gromacs: http://merlino.mi.infn.it/~plumed/PLUMED/Home.html you can perform US and Metadynamics calculations. Hope it helps and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di nishap.pa...@utoronto.ca [nishap.pa...@utoronto.ca] Inviato: venerdì 6 agosto 2010 17.08 A: gmx-users@gromacs.org Oggetto: [gmx-users] Conformational sampling Hello, I would like to do conformational sampling for my simulation of one glycine in its zwitterionic form in water and obtain a PMF curve to see if the system is equilibrated and that all possible torsions are covered for my 100ns run. I am not sure how to approach this issue. Is there a tutorial I can follow? Do I need to do umbrella sampling and use WHAM to extract PMF? I would appreciate some help! Thanks. Nisha P. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permi...@hsr.it - www.5xmille.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)
Dear all, I have performed a MD of a polymer chain interacting on a carbon nanotube using gromacs 4.0.7. I need to evaluate the potential energy of the polymer alone, during the dynamic, so to compare with its potential energy in vacuo. During the dynamic, the CNT was frozen, and I used exclusions groups to avoid to calculate CNT CNT non bonding interactions (I assume the bonds and angles potentials are computed anyway). Looking at the mailing list, I have used the following method: 1) use make_ndx to create a group system containing only the atoms for the polymer 2) Create a new simulation file:tpbconv -s original.tpr -n index.ndx -o rerun.tpr 3) adjust the trajectory according to the new simulation file: trjconv -f totaltrj.xtc -n index.ndx -s rerun.tpr -o rerun.xtc 4) analyze the trajectory: mdrun -s rerun.tps -rerun rerun.xtc everything is performed without errors, but, when I use g_energy to evaluate the energy of the polymer, I get something like: Statistics over 1501 steps [ 0. thru 3.0020 ps ], 7 data sets All averages are over 15001 frames Energy Average RMSD Fluct. Drift Tot-Drift -- - Angle 1630.1861.535661.0703 -0.000872146 -26.1644 Ryckaert-Bell. 233.04945.135834.5826 -0.00334919 -100.476 LJ-14 669.90720.079719.9169 -0.000294607 -8.8382 Coulomb-14 637.18716.292116.1707 0.000229164 6.87492 LJ (SR) 0 0 0 0 0 Coulomb (SR) 0 0 0 0 0 Potential 3170.3384.065475.4238 -0.00428678 -128.603 The question is: why the short range lennard-jones and short range coulombic interactions are zero? those are the usual option from 1 to 8: 2 Angle3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Coulomb-(SR) 8 Potential They are present for the orginal dynamic on CNT as well as in the dynamic in vacuo. hope in some answers. Thanks Andrea -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)
Mark, thank you for the fast reply. My original mdp, the one I used to run the dynamics is nstcgsteep = 1000 nbfgscorr= 10 emstep = 0.02 emtol= 10 dt = 0.002 nsteps = 1500 comm-mode= none nstcomm = 1 comm_grps= system nstxout = 1000 nstvout = 1000 nstfout = nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc_grps = system energygrps = CNT pcl nstlist = 10 ns_type = grid pbc = xyz rlist= 1.5 coulombtype = cut-off rcoulomb = 1.5 vdwtype = cut-off rvdw = 1.5 periodic_molecules = yes tcoupl = nose-hoover tc-grps = system tau_t= 0.5 ref_t= 300 Pcoupl = no pcoupltype = isotropic tau_p= 5.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = -1 constraints = all-bonds constraint_algorithm = LINCS lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 freezegrps = CNT freezedim= Y Y Y nwall= 0 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 ewald_geometry = 3d energygrp_excl = CNT CNT with this I have created, of course the tpr used to run the dynamic: runmd.tpr. With make_ndx, I have an index file containing only the pcl group. using this index file, i have created the new tpr, rerun.tpr, from the original runmd.tpr file using tpbconv. as far as I see, the only exclusion is for the CNT CNT groups (last line of the mdp file above). a gmxdump of rerun.tpr gives me this info about groups (at the end of the file) Group statistics T-Coupling : 756 (total 756 atoms) Energy Mon. : 756 0 0 (total 756 atoms) Acceleration: 756 (total 756 atoms) Freeze : 756 0 (total 756 atoms) User1 : 756 (total 756 atoms) User2 : 756 (total 756 atoms) VCM : 756 (total 756 atoms) XTC : 756 (total 756 atoms) Or. Res. Fit: 756 (total 756 atoms) QMMM: 756 (total 756 atoms) If this is not helping you, please can you tell me what else you need? Again, thanks. cheers, Andrea In the absence of information about your ensemble (from your .mdp file or a description, hint hint) I'd guess it's because you've excluded all the non-bonded interactions for which you had non-zero parameters defined. 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/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/mailing_lists/users.php -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)
I found something: apparently, I need to remove the energygrp_excl = CNT CNT from the original mdp, generate a new tpr with this modified mdp and grompp, and then use tpbconv to create the simulation file for the subsystem. my energy groups are still CNT and pcl and now g_energy gives something like this: LJ (SR)-749.54682.968663.7099 0.00613714 184.114 Potential2214.789.275189.1628 0.000516773 15.5032 LJ-SR:pcl-pcl 0 0 0 0 0 but still, LJ-SR:pcl-pcl is 0... should not be the same as LJ(SR)?... does not make too much sense. Summarizing what i did: 1) edit the mdp file, remove the groups in energygrp_excl, even if not used in the subsytem Just to clarify, comparing the new mdp with that posted before, the only difference is: energygrp_excl = --- energygrp_excl = CNT CNT 2) create the index file for the subsystem 3) rerun grompp to create the new tpr for all the system, without energygrp_excl 4) use the new tpr with tpbconv to create the simulation file for the subsystem 5) adjust the trajectory 6) run mdrun -rerun andrea -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] pdb gro files
I don't think the atom number is the problem. I also have systems with more than 9 atoms, and in the gro file the atom number after 9 is reset to 0, but that was never a problem for the simulations. I would check the parameters again, but I don't have a more exact answer to your problem. 2010/3/5 Carla Jamous carlajam...@gmail.com Hi, please I'm having a problem while running a minimisation. I prepared my system with pdb2gmx and generated .pdb files. From the last pdb file, I did grompp generated the tpr file that I used to start my minimization. At the 46th step, I encountered the problem:water molecule cannot be settled. I looked at the pdb file and found that many water residues have the same number because above residue , it restarts to count residue 0, 1, etc... I prepared the same system but I generated .gro files instead of .pdb started my minimization. But did't encounter the same problem. I looked at the gro file here, it's the atomic number that can't be above 9. So did anyone encounter this problem before, if yes, please do you have a solution to propose? Thanks Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] NVE of water
Thank you for your hints. I'll give it a try right now. Regards, Andrea 2010/3/1 Berk Hess g...@hotmail.com Hi, Shake is not relevant for water and also a time step of 2 fs should be fine. The cut-off's are the problem. You have a buffer size of 0.1 nm, which is already smaller than 2 times the distance from the center of geometry of a water molecule to a hydrogen. You need some additional distance for water diffusion. I would use a buffer of 0.25 to 0.3 nm. You don't list you coulombtype setting. Use pme (or if you want perfect energy conservation: pme-switch), you can also use reaction-field-zero if you really don't want to use PME. Then use nstlist=-1, run a short simulation and check in at the end of your log file that the neighbor list lifetime is somewhere between 5 and 20 steps. We should have a wiki entry for such details. Maybe there is one, but I was too lazy to check or make one. Berk Date: Mon, 1 Mar 2010 09:16:36 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title = NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol = 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t = 0.1 ref_t = 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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/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/mailing_lists/users.php -- New Windows 7: Find the right PC for you. Learn more.http://windows.microsoft.com/shop -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] NVE of water
Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title= NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout= 0 nstlog = 5000 nstenergy= 5000 nstlist = 10 ns_type = grid rlist= 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t= 0.1 ref_t= 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] xpm2ps tick display
Hi All, I so silly question: I have an xpm file from g_sham (gibbs energy from PCA) and I would like to convert to eps by xpm2ps. Everything goes fine except that I cannot display the tick on the postscript file!! The command I use is xpm2ps -f file.xpm -o file.eps -rainbow red -di in.m2p This is my in.m2p blackwhite = no ; Obsolete titlefont= Times-Roman ; A PostScript Font titlefontsize= 20 ; Font size (pt) legend = yes ; Show the legend legendfont = Times-Roman ; A PostScript Font legendlabel = ; Used when there is none in the .xpm legend2label = ; Used when merging two xpm's legendfontsize = 14 ; Font size (pt) xbox = 2.0 ; x-size of a matrix element ybox = 2.0 ; y-size of a matrix element matrixspacing= 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box x-major = 1; Major ticks on x axis every .. frames x-minor = 0.5 ; Id. Minor ticks x-firstmajor = 0; First frame for major tick x-majorat0 = no ; Major tick at first frame x-majorticklen = 8.0 ; x-majorticklength x-minorticklen = 4.0 ; x-minorticklength x-label = ; Used when there is none in the .xpm x-fontsize = 16 ; Font size (pt) x-font = Times-Roman ; A PostScript Font x-tickfontsize = 10 ; Font size (pt) x-tickfont = Helvetica; A PostScript Font y-major = 1 y-minor = 0.5 y-firstmajor = 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 16 y-font = Times-Roman y-tickfontsize = 10 y-tickfont = Helvetica Any help_?? thanks in advance andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Adding ions
The problem I was facing earlier: in the force field files (I am ussing ffG53a6) the ions are named NA+, CL-, for example, so with capital letters. Genion will add to the topology the ions named by default Na or Cl, unless you use the options -pname and/or -nname to name the ions. I do so and I have no mismatch of ionsname in different files. I hope this helps. Regards Andrea 2009/11/17 Arden Perkins perki...@eou.edu I am an undergraduate student and I am still learning to use GROMACS. When I add my ions to the solution (using genion) by the procedure described in the funnel web spider tutorial the .gro and .top files do not match. I tried subtracting solvent molecules but they still dont match and I can't continue. What am I doing wrong? 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_sas with pbc
Hi all, I've already simulated 27 organic molecules in a cubic solvent box. Now I would like to calculate the SAS of this system. I've a tpr and a trr with only the molecules inside (without water). I'm using gromacs 4.0.5. I've added the box dimension infos to the trr using the command: trjconv -f ../../original_multi3000.pdb -o new.trr -s reference.pdb -box 7.3973 7.3973 7.3973 In the reference.pdb I've also the CRYST informations. I've modified the gmx_sas.c to bypass the check that turn off automatically the PBC if solvent molecules are not present. Unfortunately I've seen that the results with and without taking into account the PBC are identical. So my questions are: 1) Is it possible to use the g_sas tool to calculate the SAS of this kind of system? 2) There are some tricks or trasformations or missing informations in my input(s) that I could fill before running the analysis? 3)Should I use another type of box? Trasform the trajectory with some pbc keywords (I've also tried -ur compact without luck)... Thanks in advance and sorry for the long message Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Dealing with non-aminoacid residues
Hi Pablo, I would write .rtp entries and so on for each monomer. You copy the modified files into your working directory. Have a great day, Andrea 2009/10/6 Englebienne, P. p.englebie...@tue.nl Hi all, I’m looking to perform simulations on a series of synthetic co-polymers containing a variety of building blocks. I will be testing different sequences of the monomers, therefore I am looking for a way to streamline the generation of the topologies. I have been reading Chapter 5 of the manual, but I’m still a bit puzzled about how to proceed to build topologies for my system. Should I make an .itp file for each monomer? Or generate .rtp, .hdb, .tdb and .atp files for all the possible monomers I will be using? In the case of the latter, how can I direct GROMACS to read a local copy of the databases instead of a global one? I’ll appreciate any pointers in this direction. Thanks! -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven Univeristy of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 Progress is made by lazy men looking for easier ways to do things. - Robert A. Heinlein ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] copper cluster bond to histidines
Dear all,
I am going to run some MD simulation of a protein bearing a copper cluster (3
Cu2+ nominally charge
2+) coordinates to histidine residues. As far as concerning the importance of
this cluster in the
enzymatic activity (this would require QM/MM), my issue is how to interpret the
whole system
[HIS_{2}-Cu2+]_{3} in term of force field. From literature and from previous
posts in this mailing
list, in MD system similar to mine (aminoacid coordinating ions) are treated as
an unique residues
(i.e. HEME group). My first try was to perform MD without restraints on Cu2+,
but unfortunately at
100K (I am doing an equilibration from 100K to 300K) after few ps one of the
Cu2+ left already its
position (basically it is flying away).
Second try was to put restraints on the system between the Cu2+ and the N-HIS.
However, my doubt is
how bad is this assumption respect to the possibility to consider the whole
system Cu2+-HIS as an
unique residue in the topology file. I am aware that for the latest hypothesis
I should reconsider
all the properties (i.e. charges, angles, etc ...), so a long way and hard
work. Think about that I
need to put a O2 molecule inside of the Cu2+ cluster in a second study.
Any suggestion, comments and anything else are very welcome.
Thanks in advance
Regards
andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
---
-
La tua mano puo' lasciare un segno importante.
Dona il tuo 5 per mille al San Raffaele di Milano.
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei redditi
Finanziamento della ricerca sanitaria
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org.
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] copper cluster bond to histidines
Hi Tsjerk,
thanks for the usual useful suggestions! Probably I will go for that, add an
harmonic bonds between
Cu2+ and N-HIS and I will think how to hand the charges too.
Probably this is the less worst solution for now.
Thank a lot,
Regards
andrea
Tsjerk Wassenaar wrote:
Hi Andrea,
You're probably best off 'fixing' the copper to the protein, meaning
introducing bonds at least (harmonic, type 6?). With these bonds you
can to some degree account for the effects of polarization and such on
the interatomic distances, which are likely more difficult to model
reparameterizing the non-bonded interactions. You should also
definitely consider that there is considerable polarization and charge
transfer in such metal clusters, which means that you should probably
attenuate the charges of the copper as well as of the ligating atoms.
For the ligation geometry you can try to rely on size-exclusion
effects of the ligands, but copper may prove nasty, in which case you
also need to set parameters for angles and maybe for dihedrals. Not
for naught that newbies are usually discouraged for performing
simulations like these (exotic species)... But you had already
considered that.
Hope this helps,
Tsjerk
On Wed, Aug 12, 2009 at 12:40 PM, andrea
spitalerispitaleri.and...@hsr.it wrote:
Dear all,
I am going to run some MD simulation of a protein bearing a copper cluster
(3 Cu2+ nominally charge
2+) coordinates to histidine residues. As far as concerning the importance
of this cluster in the
enzymatic activity (this would require QM/MM), my issue is how to interpret
the whole system
[HIS_{2}-Cu2+]_{3} in term of force field. From literature and from previous
posts in this mailing
list, in MD system similar to mine (aminoacid coordinating ions) are treated
as an unique residues
(i.e. HEME group). My first try was to perform MD without restraints on
Cu2+, but unfortunately at
100K (I am doing an equilibration from 100K to 300K) after few ps one of the
Cu2+ left already its
position (basically it is flying away).
Second try was to put restraints on the system between the Cu2+ and the
N-HIS. However, my doubt is
how bad is this assumption respect to the possibility to consider the whole
system Cu2+-HIS as an
unique residue in the topology file. I am aware that for the latest
hypothesis I should reconsider
all the properties (i.e. charges, angles, etc ...), so a long way and hard
work. Think about that I
need to put a O2 molecule inside of the Cu2+ cluster in a second study.
Any suggestion, comments and anything else are very welcome.
Thanks in advance
Regards
andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
---
-
La tua mano puo' lasciare un segno importante.
Dona il tuo 5 per mille al San Raffaele di Milano.
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei redditi
Finanziamento della ricerca sanitaria
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Per saperne di piu': 5permi...@hsr.it o vai sul sito
http://www.5xmille.org.
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
---
-
La tua mano puo' lasciare un segno importante.
Dona il tuo 5 per mille al San Raffaele di Milano.
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei redditi
Finanziamento della ricerca sanitaria
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org.
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests
R: [gmx-users] Supercomputing Center
Hi there, for european users you may think to apply to hpc-europa (http://www.hpc-europa.eu/) and http://www.deisa.eu/ Regards andrea --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di Negar Ashari Astani [negarast...@gmail.com] Inviato: domenica 9 agosto 2009 10.43 A: Discussion list for GROMACS users Oggetto: [gmx-users] Supercomputing Center Hi gmx users Is there any worldwide online supercomputing center for running the gromacs mdruns? I have 6 runs, each of them take about a month on a quadracore computer! I need something a bit faster! I'll be grateful if someone could introduce me somewhere! thank you all -- Negar Ashari Astani - La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi Finanziamento della ricerca sanitaria il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] continuing a MD simulation on different architectures
Dear all, is there any problem to continue (extend) a simulation using a different architecture hardware? I have a set of simulations coming from xt4 and xt5 architecture (eepc and csc clusters) and I would like to extend the simulation step on my cluster (intel) using the previous cpt file and generating the new tpr on my cluster. I did it and it runs, however I was wondering about the physical and chemical reliability. thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- - La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi Finanziamento della ricerca sanitaria il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] continuing a MD simulation on different architectures
Hi, thanks for the answer. One thing: what do you mean for but not binary identical? From the manual mdrun says: The only disadvantage of dynamic load balancing is that runs are no longer binary reproducible, but in most cases this is not important this sentence is also not very clear to me. thanks in advance Regards andrea Berk Hess wrote: Hi, As mdrun will tell you in stderr and md.log when you try continuing, you will have exact continuation, but not binary identical (which you would not have anyhow if you use dynamic load balancing). Exact continuation mean perfect physical and chemical reliability. Berk Date: Thu, 2 Apr 2009 13:28:21 +0200 From: spitaleri.and...@hsr.it To: gmx-users@gromacs.org Subject: [gmx-users] continuing a MD simulation on different architectures Dear all, is there any problem to continue (extend) a simulation using a different architecture hardware? I have a set of simulations coming from xt4 and xt5 architecture (eepc and csc clusters) and I would like to extend the simulation step on my cluster (intel) using the previous cpt file and generating the new tpr on my cluster. I did it and it runs, however I was wondering about the physical and chemical reliability. thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- - La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi Finanziamento della ricerca sanitaria il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org. ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messengerhttp://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- - La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi Finanziamento della ricerca sanitaria il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] grompp errors
i have a problem with gromp someone can elp me? thanks.. error_grompp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Variance in ED
Dear Dr. Wassenaar, many thanks for your kind reply. Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Variance in ED
Hi all, perhaps a silly question but i didn't find the correct way to calculate the variance explained by each eigenvec in ED analysis. Could someone point me out to a correct tool/option to use. I'm using gmx v3.3. Many thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?
Hi Andrew, I would do it with editconf with the same options. Regards Andrea 2009/3/11 Andrew Voronkov drugdes...@yandex.ru: Dear GROMACS users, is there a possibility to convert .gro files directly to PDB? Or I can do it only with .tpr? I've tried gro2pdb -f conf.gro -o conf.pdb but it doesn't work. Best regards, Andrew ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Rtp for polymer.
I connect the monomers by adding a bond in the rtp entry, in which the first atom of the next residue is given with + (you can also connect with the previous residue with - in front of the last atom). Sorry to explain this in a very confuse way. Better look at the example bellow (for polystyrene): [PS] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] ;-CHCH2 gb_ (you put the appropriate bond from the ff*_bon.itp file) CH2 CH gb_ CH CB gb_ CB CG1 gb_ CG1 CG2 gb_ CG2 CG3 gb_ CG3 CG4 gb_ CG4 CG5 gb_ CG5 CB gb_ CH +CH2gb_ [angles] ... [impropers] ... [dihedrals] ... (angles, impropers and dihedrals were defined accordingly, but not listed here) I hope that will help. Andrea 2009/2/5 varsha gautham varsha.gautha...@gmail.com: Hello justin, Am sorry to say that its not useful.But what i mean is that the rtp constructed manually is building up the polymer and generating topology files and gro files. But when i look into the gro file with vmd the connectivity between each of the monomer is not built.That is my polymer consists of 10 monomer units with ben and primary amine unit as a block polymer. How can i include the connectivity information between these two in a rtp file?I can include that in session called bonds. But how to do that??And i want some help regarding the workflow that is how gromacs interpreting each of the rtp, atp ,ffnb.itp,ffbon.itp??I want to know that in a sequential order.are there any materials available other than manual..If so please let me know Thanks in advance. -krithika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] PBC only in xy direction
Hi gmx-users, We are using the version 3.3.3. Is there also a posibility to have pbc only in xy direction (as I saw it is possible in Gromacs 4.0)? The manual says nothing about that. Thank you in advance. Best regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PBC only in xy direction
Hi Berk, that is a good idea. Thank you for your answer. Cheers, Andrea 2008/12/11 Berk Hess [EMAIL PROTECTED]: Hi, This is not possible in 3.3. But in practice you almost never need this, since it is far more efficient to use pbc=xyz and have a slab of vacuum in between the periodic images in z. Berk Date: Thu, 11 Dec 2008 10:30:55 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] PBC only in xy direction Hi gmx-users, We are using the version 3.3.3. Is there also a posibility to have pbc only in xy direction (as I saw it is possible in Gromacs 4.0)? The manual says nothing about that. Thank you in advance. Best regards, Andrea ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] system explodes
I am simulating one chain of PS. The box is produced by pdb2gmx. If I run simulations with timestep 0.1 fs up to 0.4 fs everything seem to be ok. With 1 fs (which should be a normal time for my system) I would get the following warning: Warning: 1-4 interaction between 290 and 299 at distance 108.224 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file The parameters I use are the following: title= PS cpp = /lib/cpp integrator = md dt = 0.0001; ps ! nsteps = 1 ; total 10 ps nstlist = 10 nstxout = 100 nstvout = 100 nstenergy= 100 unconstrained-start = yes nstxtcout= 50 nstlog = 50 constraints = none ns_type = grid vdwtype = Cut-off fourierspacing = 0.055 ; Lbox/0.055 ~ 50 rlist= 0.9 rvdw = 1.2 tc_grps = system tcoupl = berendsen tau_t= 0.1 ref_t= 540 Pcoupl = no optimize_fft = yes the rest is set default Did I miss something? What goes wrong? Any help and/or comments are really appreciated. Thank you! Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] system explodes
Thank you. I will do so. kind regards, Andrea 2008/11/11 Justin A. Lemkul [EMAIL PROTECTED]: Andrea Muntean wrote: I am simulating one chain of PS. The box is produced by pdb2gmx. If I run simulations with timestep 0.1 fs up to 0.4 fs everything seem to be ok. With 1 fs (which should be a normal time for my system) I would get the following warning: Warning: 1-4 interaction between 290 and 299 at distance 108.224 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file The parameters I use are the following: title= PS cpp = /lib/cpp integrator = md dt = 0.0001; ps ! nsteps = 1 ; total 10 ps nstlist = 10 nstxout = 100 nstvout = 100 nstenergy= 100 unconstrained-start = yes nstxtcout= 50 nstlog = 50 constraints = none ns_type = grid vdwtype = Cut-off fourierspacing = 0.055 ; Lbox/0.055 ~ 50 rlist= 0.9 rvdw = 1.2 tc_grps = system tcoupl = berendsen tau_t= 0.1 ref_t= 540 Pcoupl = no optimize_fft = yes the rest is set default Did I miss something? What goes wrong? You are running a very high temperature with no bond constraints. I would expect you would need a very small timestep (like 0.1 fs) to get reasonable dynamics. Try using constraints. -Justin Any help and/or comments are really appreciated. Thank you! Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] .mdp file
I thought so. Thank you very much! Cheers Andrea 2008/11/10 Justin A. Lemkul [EMAIL PROTECTED]: Andrea Muntean wrote: Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I want to run another simulation, with the same input, only with small changes in the mdp file (like number of steps or so), do I have to each time modify the input .mdp and run grompp, or is it enough if I modify mdout.mdp? No. The mdout.mdp file is output, a record of all the simulation parameters, including the ones you accepted as defaults by not explicitly entering into your grompp.mdp file (the input). If you want to run different simulations, you need to modify your input, or else these new parameters will never reach the .tpr file and you will be running the same thing over and over again. -Justin Best regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .mdp file
Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I want to run another simulation, with the same input, only with small changes in the mdp file (like number of steps or so), do I have to each time modify the input .mdp and run grompp, or is it enough if I modify mdout.mdp? Best regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parameters
Dear users, I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and the following parameters (only a few are given): ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 125000 comm-mode= Linear nstcomm = 1 nstlist = 10 ns-type = Grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 I recently noticed from the manual that the nstlist should be 5 with gromos 96 ff. I have a couple of questions. 1. should this be 5 with a 0.001 timestep or with a 0.002 timestep 2. As I have done a lot of work using these parameters I was really looking for some suggestions/advice as to whether I can use any of my data - I;m really clinging onto hope here! And as to how 'badly' this choice/mistake will have affected my work. Thanks, Les ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dihedrals again
Hi all, I did some work on thise dihedrals for polystyrene, and I simplified my version now, using also the inspiration from PHE residue. My problem now is that for the dihedral around the CH2-CH bond in the inner monomer (PS thus) I define in the rtp -CH CH2 CH +CH2gd_17 but in the top fileinstead of 2 9 10 17 gd_17 I get this: 2 9 10 11 (without any parameter). This make me think that pdb2gmx does not count the dihedral as I defined it (why?) but puts a default dihedral there, without any parameter. I am right? What would be a solution for that? My dihedrals are now defined as follows (it helps if you really draw the molecule): the entries in the rtp file for first (PS1), inner (PS) and last (PSN) monomer: [PS1] [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_17 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 [PS] [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_17 -CH CH2 CH +CH2gd_17 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 [PSN] [dihedrals] ;in the chain - 3-fold (n=3) -CH CH2 CH CH3 gd_17 ;around CH-CB - 2-fold (n=2) CH2 CH CB CG5 gd_1 The results for trimer in the top file. [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 1 2 3 8 1gd_1 1 2 910 1gd_17 2 91011 1 9101116 1gd_1 9101718 1gd_17 10171825 1gd_17 17181924 1gd_1 Best regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: dihedrals again
Remark: if I change that dihedral with -CHCH2 CH CBgd_17, that it gives again 2 9 10 11 , but this time with gd_17, as it should do. But why it does not work with the other definition? Does it have to do with the fact that in the dihedral I have atoms belonging to 3 residues? And are the 2 definitions (with +CH2 and CB at the end) equivalent, taking in acount that we define also an improper of type gi_2 around the CH atom? Cheers, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dihedral not counted?
Hi all, I defined my residues for Polystyrene (first, last and inner monomers), with the coresponding bonds, angles, dihedrals and impropers, including also the conectivities (as + and - atoms of the next or previous residue). Pdb2gmx runs without error or warning, but it counts less dihedrals then I would expect. I did run the same for dimer and trimer. For dimer is ok, for trimer starts to count 1 dihedral less, and for the chain with 80 monomers corespondingly 78 dihedrals less, which means that the error should be in the inner residue. I checked many times, but the dihedral which is missing in the .top file is defined in the .rtp. So I have really no clue what is wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me. Please give me a good idea :o) Thanks in advance. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
Hi Justin, here are the relevant parts, as pdf files. I miss a dihedral between the atoms 2, 9, 10 and 17, which corresponds to the -CH CH2 CH +CH2 dihedral in the PS residue in the RTP entry. For the trimer I should have 26 dihedrals, but in the TOP file I get only 25 (I mean only the proper dihedrals, the impropers are OK). Thanks for your help. Andrea RTP.pdf Description: Adobe PDF document TrimerTOP.pdf Description: Adobe PDF document ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
CH CB gd_16 -CH CH2 CH CH3 gd_16 ;around CH-CB - 2-fold (n=2) CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB CH3CH2 gi_1 CH CH3 CH2CB gi_1 CH CH2 CB CH3 gi_1 [dihedrals] ;in the chain - 3-fold (n=3) -CH CH2 CH CB gd_16 -CH CH2 CH CH3 gd_16 ;around CH-CB - 2-fold (n=2) CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 And the .top file for the trimer, only the [atoms] and [dihedrals] (only the proper dihedrals) part: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1CH3 1PS1CH3 1 0 15.035 ; qtot 0 2CH1 1PS1 CH 1 0 13.019 ; qtot 0 3 C 1PS1 CB 1 0 12.011 ; qtot 0 4CR1 1PS1CG1 1 0 13.019 ; qtot 0 5CR1 1PS1CG2 1 0 13.019 ; qtot 0 6CR1 1PS1CG3 1 0 13.019 ; qtot 0 7CR1 1PS1CG4 1 0 13.019 ; qtot 0 8CR1 1PS1CG5 1 0 13.019 ; qtot 0 9CH2 2 PSCH2 2 0 14.027 ; qtot 0 10CH1 2 PS CH 2 0 13.019 ; qtot 0 11 C 2 PS CB 2 0 12.011 ; qtot 0 12CR1 2 PSCG1 2 0 13.019 ; qtot 0 13CR1 2 PSCG2 2 0 13.019 ; qtot 0 14CR1 2 PSCG3 2 0 13.019 ; qtot 0 15CR1 2 PSCG4 2 0 13.019 ; qtot 0 16CR1 2 PSCG5 2 0 13.019 ; qtot 0 17CH2 3PSNCH2 3 0 14.027 ; qtot 0 18CH1 3PSN CH 3 0 13.019 ; qtot 0 19 C 3PSN CB 3 0 12.011 ; qtot 0 20CR1 3PSNCG1 3 0 13.019 ; qtot 0 21CR1 3PSNCG2 3 0 13.019 ; qtot 0 22CR1 3PSNCG3 3 0 13.019 ; qtot 0 23CR1 3PSNCG4 3 0 13.019 ; qtot 0 24CR1 3PSNCG5 3 0 13.019 ; qtot 0 25CH3 3PSNCH3 3 0 15.035 ; qtot 0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 1 2 3 4 1gd_1 1 2 3 8 1gd_1 9 2 3 4 1gd_1 9 2 3 8 1gd_1 1 2 910 1gd_16 3 2 910 1gd_16 2 3 4 5 1 2 3 8 7 1 2 91011 1gd_16 9101112 1gd_1 9101116 1gd_1 17101112 1gd_1 17101116 1gd_1 9101718 1gd_16 11101718 1gd_16 10111213 1 10111615 1 10171819 1gd_16 10171825 1gd_16 17181920 1gd_1 17181924 1gd_1 25181920 1gd_1 25181924 1gd_1 18192021 1 18192423 1 Cheers, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
Strange enough, those dihedrals are there, but the dihedral between atoms 2 9 10 and 17 is missing (in the main chain), altough defined in the PS residue (as -CH CH2 CH +CH2). I am still clueless... Greetings, Andrea 2008/10/27 Justin A. Lemkul [EMAIL PROTECTED]: Well, there's no real problem, per se. Everything that you've given pdb2gmx is in the topology; the issue is that you haven't specified any parameters for those dihedrals: CH CB CG1 CG2 CH CB CG5 CG4 2 3 4 5 1 2 3 8 7 1 Makes sense that they'd be missing. If you're dealing with polystyrene, maybe consider basing the dihedrals off of those contained in the PHE sidechain in the Gromos force field you appear to be using. -Justin Andrea Muntean wrote: Here are the .rtp entries: [PS1] [atoms] CH3 CH3 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] CH3 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle CH3 CH +CH2ga_12 CH3 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH3 gi_1 CH +CH2CH3 CB gi_1 CH CH3 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [PS] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle -CH CH2 CH ga_12 CH2 CH +CH2ga_12 CH2 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH2 gi_1 CH +CH2CH2 CB gi_1 CH CH2 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 -CH CH2 CH CB gd_16 -CH CH2 CH +CH2gd_16 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [ PSN ] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 CH3 CH3 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH CH3 gb_26 [angles] -CH CH2
Re: [gmx-users] monomer's conectivity
Thank you for your answer. If I am looking at the PDB standard format and my file, I observe that I have only one number between the type of residue and coordinates, and I suppose it is the residue current number. I am indeed missing the chain identifier code, which should be of A1 Fortran format, which I don't really understand (one carachter, but I have 32 chains, so it should be minimum A2 or I2). That I could introduce. In my pdb entries I dont define any connectors. Should they be a dummy atom, with the corresponding bond, angle, dihedhral, which after that I redefine in the tdb file? I dont think it is a visualisation artefact, because it really gives less number of bonds, corresponding to the missing intermonomeric bonds. Should I do now both (introducing a chain identifier in the pdb, but how?, and defining the intermonomeric bonds via dummy in the pdb and tdb?)? Thanks again for your help. Best regards, Andrea 2008/10/22 Mark Abraham [EMAIL PROTECTED] Andrea Muntean wrote: I have a *pdb file for a polymer box which I want to use. I defined the residues (the first, the last and the inner monomers). Pdb2gmx runs, but I obtain a soup of monomers instead of N chains a M monomers each. My problem now is how to connect the monomers. What is the best way to do so? We can't tell yet. You might have a PDB file with each residue in its own chain. You might have defined residue topologies without suitable connectors. You might be observing a visualization artefact. You might have some warnings from pdb2gmx you haven't observed yet. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] monomer's conectivity
Thank you. I hope this helps me further. My system is 32 polystyrene chains of 80 monomers. Andrea 2008/10/23 Mark Abraham [EMAIL PROTECTED] Andrea Muntean wrote: Thank you for your answer. If I am looking at the PDB standard format and my file, I observe that I have only one number between the type of residue and coordinates, and I suppose it is the residue current number. I am indeed missing the chain identifier code, which should be of A1 Fortran format, which I don't really understand (one carachter, but I have 32 chains, so it should be minimum A2 or I2). That I could introduce. Get a PDB file with just one polymer molecule and work on getting a topology for that. Walking before running :-) In my pdb entries I dont define any connectors. Should they be a dummy atom, with the corresponding bond, angle, dihedhral, which after that I redefine in the tdb file? First you need a functional *residue topology*. Check chapter 5 of the manual and look at the other force fields to see how (for example) protein force fields define the connectors with + and - prefixes. Once you've got that, then it's possible for pdb2gmx to join them head to tail (using the residue number field to indicate the breaks, and the name to match up with the topology you've defined), and you may then need either terminating residues of a different name or a .tdb entry. I dont think it is a visualisation artefact, because it really gives less number of bonds, corresponding to the missing intermonomeric bonds. Your visualization software is not reading a file format that is encoding any topology (since you haven't produced one yet). Thus it's inventing some bonds based on the coordinates. The output of pdb2gmx that contains topology information is the .top file, not the coordinate file. Should I do now both (introducing a chain identifier in the pdb, but how?, and defining the intermonomeric bonds via dummy in the pdb and tdb?)? I suppose there are some circumstances where chain identifiers might be useful, but since you haven't even told us what your monomer and system are, it's hard to help you. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] monomer's conectivity
It did work. Thank you! Cheers, Andrea 2008/10/23 Mark Abraham [EMAIL PROTECTED] Andrea Muntean wrote: Thank you for your answer. If I am looking at the PDB standard format and my file, I observe that I have only one number between the type of residue and coordinates, and I suppose it is the residue current number. I am indeed missing the chain identifier code, which should be of A1 Fortran format, which I don't really understand (one carachter, but I have 32 chains, so it should be minimum A2 or I2). That I could introduce. Get a PDB file with just one polymer molecule and work on getting a topology for that. Walking before running :-) In my pdb entries I dont define any connectors. Should they be a dummy atom, with the corresponding bond, angle, dihedhral, which after that I redefine in the tdb file? First you need a functional *residue topology*. Check chapter 5 of the manual and look at the other force fields to see how (for example) protein force fields define the connectors with + and - prefixes. Once you've got that, then it's possible for pdb2gmx to join them head to tail (using the residue number field to indicate the breaks, and the name to match up with the topology you've defined), and you may then need either terminating residues of a different name or a .tdb entry. I dont think it is a visualisation artefact, because it really gives less number of bonds, corresponding to the missing intermonomeric bonds. Your visualization software is not reading a file format that is encoding any topology (since you haven't produced one yet). Thus it's inventing some bonds based on the coordinates. The output of pdb2gmx that contains topology information is the .top file, not the coordinate file. Should I do now both (introducing a chain identifier in the pdb, but how?, and defining the intermonomeric bonds via dummy in the pdb and tdb?)? I suppose there are some circumstances where chain identifiers might be useful, but since you haven't even told us what your monomer and system are, it's hard to help you. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] monomer's conectivity
I have a *pdb file for a polymer box which I want to use. I defined the residues (the first, the last and the inner monomers). Pdb2gmx runs, but I obtain a soup of monomers instead of N chains a M monomers each. My problem now is how to connect the monomers. What is the best way to do so? Regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Converting 2-d molecule to 3-D
Hi there, have look to corina software. I dont think it is free. http://cheminf.cmbi.ru.nl/cheminf/corina/ and vivek sharma wrote: Hi there, Is there any open source package to convert 2-D structure of a molecule to 3-D structure ? If anybody have tried such thing, please suggest me te way to do the same. I am having openbabel on my system, does openbabel i shaving such functionality ? please suggest ? With thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Preparing polystyrene
I am trying to use a .pdb for a polystyrene film (32 chains with 80 monomers each). The problem is that when I start running pdb2gmx I get the error that it can not find the residues (which are of course different from those in Gromacs). What would be the best thing to do? Have somebody a pdb or rtp file for Polystyrene? Which force filed would be more apropriate (united atoms)? Thank you. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] help with installation
I want to install fftw and gromax in my directory. Everything went ok, fftw was installed without errors. When I configure gromacs I have the error: cannot find fftw3f library. I did use the CPPFLAGS and LDFLAGS. Can somebody help me? Thank you kindly in advance! Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Polystyrene box
Hello, we are trying to generate a polystyrene box. We have a homemade pdb file, but the residues are not recognised. Have somebody a good pdb file or can tell me what are the standard residues in Gromax? Any other good hints are welcome. Thanks a lot, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] T-WHAM for replica
Hello everyone, Does anyone have a script to do T-WHAM analysis of replica exchange trajectories? Any help would be great! Thanks, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group
Hi there, my system is about 200,000 atoms. we have installed the latest version (4.0_beta1) on our cluster but i get the follow error after few calculation ps : 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group similar to what reported few months ago (http://www.gromacs.org/pipermail/gmx-revision/2008-July/000213.html). Using the version 3.3.99_development_200800503 on Louhi (csc.fi) the run goes fine. In our cluster with 4.0_beta1 i am using 36 cpus (with no -dd option) whereas on louhi 64 cpus (using -dd 4 4 4 option). I hope this help in gmx debugging Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group
Hi again, in addition to the previous post, 4.0_beta1 crashes using 27 cpus and option -dd 3 3 3, whereas it goes fine using 24 cpus and not -dd option. any clue? Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cvs version and position restraints...
Thanks Berk, yes, it was an older version. And I did have separate pme nodes when posre was working. So now I'm trying out the new CVS version. Andrea On Jul 21, 2008, at 1:53 PM, Berk Hess wrote: Hi, There was a bug with PME and position restraints in the CVS version, but that has been fixed a month ago. This bug has exactly the behavior you describe, posres should work ok with separate pme nodes (nnodes = 12), but not without (1 nnodes 12). So I assume you are not using the most recent CVS version? Berk. Date: Tue, 15 Jul 2008 18:17:10 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] cvs version and position restraints... Hi everyone, I have a small DNA duplex in a dodecahedron box. Amber forcefield. Spce water. I have position restraints defined for the whole duplex in my topology. I'm running exactly the same input script on 2, 4 and on 12 cpus. The one with 12 produces a trajectory in which it is quite clear that the restraints are working: the stronger the restraints on a given set of atoms, the less these atoms move away from the equilibrium position during the simulation. With 4 and 2 cpus, it is af if no restraints are used (the whole system tumbles and moves around the box), although I do see energy terms for the restraints in the log file... I'm using the CVS version (downloaded June 4th). I'm not sure but I think I remember someone having a similar problem on version 3.2 but I don't remember how/if it was solved. I couldn't find anything on the mailing lists. Any clue about what's going on? Thanks, Andrea ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cvs version and position restraints...
Hi everyone, I have a small DNA duplex in a dodecahedron box. Amber forcefield. Spce water. I have position restraints defined for the whole duplex in my topology. I'm running exactly the same input script on 2, 4 and on 12 cpus. The one with 12 produces a trajectory in which it is quite clear that the restraints are working: the stronger the restraints on a given set of atoms, the less these atoms move away from the equilibrium position during the simulation. With 4 and 2 cpus, it is af if no restraints are used (the whole system tumbles and moves around the box), although I do see energy terms for the restraints in the log file... I'm using the CVS version (downloaded June 4th). I'm not sure but I think I remember someone having a similar problem on version 3.2 but I don't remember how/if it was solved. I couldn't find anything on the mailing lists. Any clue about what's going on? Thanks, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to edit pdb file
Hi, have look to this: http://stein.bioch.dundee.ac.uk/~charlie/software/pdb-mode/pdb-mode.html I found it very useful regards andrea Wei, Xiupeng wrote: Dear GMX users, I have a basic question. I want to put two same box in x direction. So I need increase the number of atoms and change their x coordinates,then combine it with the original one. But the file created by Excel can't be recoganized by gromacs. Is there any method in Gromacs to handle that? I also used Matlab, but it can't read pdb file correctly. Thanks. Best regards, xiupeng ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Finanziamento agli enti della ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] modify the distance constraints force constant during the simulation
Dear all, I would like to increase linearly the force constant of some distance constraints during my MD and then decrease it: 2 ps for 100 cycles with the force constant being raised by 50 kj mol^(-1) nm^(-2) 2 ps for 100 cycles with the force constant being reduced by 50 kj mol^(-1) nm^(-2) is there a way to do it with gromacs? I looked carefully in the manual and in the mailing list too, but I couldn't find an option to do this Thanks in advance, Andrea -- Andrea Bortolato, PhD Postdoctoral Associate Dept. of Structural and Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute Building 1425 Madison Avenue, Box 1677 New York, NY 10029-6574 Tel.: 212-659-5406 Fax: 212-849-2456 Email: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] benchmark: buying a new cluster
Hi all, we are going to buy a new cluster and we are in doubt about the frequency to consider. Basically, we have the possibility to buy either 18 nodes dual quad-core (18x8 cores) bearing Intel-Xeon E5430 2.66 MHz and FSB 1333 MHz or 15 nodes dual quad-core (15x8 cores) bearing Intel-Xeon E5462 2.8 MHz and FSB 1600 MHz. The latest seems to be **only** 10% faster then the first. However, thinking to the new gromacs4, we are in doubt about the best solution. Is it better to have a **nominal** 10% cpu faster or to have 24 further cores? Thanks in advance for any welcome suggestion, Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Finanziamento agli enti della ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Mn parameters
Hi all, sorry for the previous wrong links (Thanks to Mark): http://www.gromacs.org/pipermail/gmx-users/2002-April/001333.html http://www.gromacs.org/pipermail/gmx-users/2002-March/001000.html http://www.gromacs.org/pipermail/gmx-users/2006-July/022999.html Regards, andrea andrea spitaleri wrote: Hi all, from a my previous post (http://www.gromacs.org/component/option,com_wrapper/Itemid,165/), I switched the Mn2+ cation in Ca2+ and I have run some standard MD. Now, unfortunately, it seems that the cation type has a biological relevance in the activity of my protein. So I went back to the Mn and I have done some lit and just found an interesting paper about abinitio calculation on my protein interacting with Mn2+ (j. phys. chem. B. 2007, 111, 9099-9103). The force field used in my calculation is OPLS and I am wondering if anyone have developed LJ parameters for Mn2+ for this FF. Previous post are: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ and http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226433497/4922 Fax: 0039-0226434153 --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Mn parameters
Hi all, from a my previous post (http://www.gromacs.org/component/option,com_wrapper/Itemid,165/), I switched the Mn2+ cation in Ca2+ and I have run some standard MD. Now, unfortunately, it seems that the cation type has a biological relevance in the activity of my protein. So I went back to the Mn and I have done some lit and just found an interesting paper about abinitio calculation on my protein interacting with Mn2+ (j. phys. chem. B. 2007, 111, 9099-9103). The force field used in my calculation is OPLS and I am wondering if anyone have developed LJ parameters for Mn2+ for this FF. Previous post are: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ and http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226433497/4922 Fax: 0039-0226434153 --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Vacancies
Post Doc Position at Molnac www.molnac.unisa.it An exceptional Post Doc candidate is required to carry out a collaborative research project between the group of Dr. Giuseppe Milano and an a well known industrial partner (*ST Microelectronics*). The project involves the development and application of new molecular simulation methods at atomistic and coarse-grained level to polymeric materials relevant in Nanoelectronics. Experience in modifying and writing Molecular Dynamics and/or Monte Carlo codes (not simply using packages) is required. The appointment is for one year with the possibility of a yearly renewalthereafter. The research group has good computational facilities, and friendly atmosphere. Computational facilities at Molnac include local workstations, two beowulf cluster, and access to large computer resources via membership at the main supercomputer centres in Europe. Please send a CV and names of 3 references to Dr. Giuseppe Milano ([EMAIL PROTECTED]) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xpm to ascii
Hi all, I would like to have a txt file from an xpm matrix generated by g_rms or g_cluster. Someone has already done this? I've seen in the previous posts some hints about hacking the code or scripts usefull for g_covar...but I'm not so confortable and expert to do such things without a step by step guru guide... Thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rms
Hi and thanks for answering to my previous question. Now I'm calculating the rmsd between two trajectories (-f2 option). One is made by 2200 frames and the other has 33 frames..Now I've some doubt about the output (rmsd.xvg), cause this file has only two columns with 2200 rows ...i was imaging that it should have 2200 rows and 33 columns, am I wrong? The second question is something that is already been asked before..it could be usefull to obtain the matrix 2200 x 33 in a human readable file. Is it possible without hacking the code? Perhaps using external scripts? Thanks a lot again Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rms
Hi, You should be getting such a 2200x33 matrix. My guess is that the command line or files that you're using are not what you think they are :-) my command line is g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin Note that the pdbs (traj and ref) have the same number of atoms (same structure). During the calculation i can see that it is creating the 2200x33 matrix, but on the rmsd.xvg i find only two columns. From the xpm and dat files i can't extract the matrix (i don't know) to a text file. I hope this could clarify better my question Thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rms
Hi again, If you read g_rms -h like I suggested last time, you'll see that -f2 and -s serve the same purpose with the former using a trajectory and the latter a single structure. That document doesn't say what happens when you use both... but the operation you're trying to do doesn't need both! the -h option is my standard first step when i use all the gmx-tools and I've read and done it like every time. I've tried to use -f2 option without using the -s and it comes out with the error topol.tpr not found so it's not so optional, but it's needed also when using the -f2 option.. I've alsto tried to use the -s with my traj without using the -f2 option but it creates a matrix 2200x2200. However the problem still remain unsolved or misunderstanded. If i use the my only working command line g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a mean of all the rmsd calculated for that frame in respect to the other 33 refs? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rms
So does the -Rmat option not produce a human-readable text file? Hi, unfortunately I can't see this option in g_rms. I'm using the v 3.3.1 and also on the reference page online there is not -Rmat. Am i missing something? Thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_cluster questions
Hi all, I'm using this tool to cluter 2200 structures in this way: fitting on the backbone, rmsd calculated on key residues (10) of the Binding site. Now I created the correct group in the index file and using the g_cluster giving the trajectory as input i can only choose one group for fitting and rmsd calculation..So I've tried also to fit the trajectory before to use it in g_cluster with the option -fit (to jump the fitting step and choose directly the group for the rmsd calculation; i've tried also -fit no) but it seems that the program ignore it (on screen, during the group selection it asks for the fitting and Rmsd group and on -fit line i can see yes)...SO my next strategy is been to calculate the xpm matrix with g_rms, fitting on the backbone and calculating the rmsd values on the Bindingsite group. Then I've used the xpm as input in the g_cluster, but it asks me however for a group for the LSfitting..could someone explain me this behaviour? Is my procedure correct for my purpose? Is normal that g_cluster does not accept the -fit option? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] psf 2 top
Hi all, I've performed my MD simulations using the charmm FF and NAMD (so pdb,psf and dcd files). Now i would like to use the great GMX analysis tools. I've successfully converted the dcd file in trr (using catDCD). Now the next step I'd like to do is the psf to top conversion. I've seen on the vmd site that a top2psf script is present but it not do the reverse conv that i need. I would prefer to not pass through pdbs.I would like to do this to not loose corrispondences of atoms and to not miss parameters for not typical residues that I'm using (like phosphrilated serines). Is there someone that could help me on this topic? Thanks in advance Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_mindist -pi option
Hi again, since I did not get answer I double checked my trr file. In case I calculate the minimum distance of the periodic image for each component of my complex, I get reasonable value of it (3.0 and 2.9 nm), whereas if I consider the whole system (protein) I get this strange result of 0.17 nm. Any clue? thanks again Regards andrea andrea spitaleri wrote: Hi there, I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting periodic image of 3.0 nm, using PME and rlist=rvdw=rcoulomb=0.9. Now, I use to check the pi dist during my simulation in order to make sure that the box is larger enough. After 6ns I get this result: 03.018 4.711 6.555 6.555 6.555 30 2.791 4.514 6.557 6.557 6.557 60 2.721 4.270 6.555 6.555 6.555 90 2.762 4.378 6.554 6.554 6.554 4620 3.017 4.042 6.558 6.558 6.558 4650 0.173 9.080 6.548 6.548 6.548 4680 2.700 3.949 6.561 6.561 6.561 4710 2.881 4.113 6.560 6.560 6.560 ... 6000 2.939 4.049 6.556 6.556 6.556 So it seems that there is a spike around 4650 ps of a very low distance (quite worrying me). Any hints? is it true this value or is it pbc artefact? Thanks in advance Regards, and ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2 -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito w w w . 5 x m i l l e . o r g ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito w w w . 5 x m i l l e . o r g ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_mindist -pi option
Hi Miguel, that's it. Visualizing the system in vmd I see that at the point the two peptides are in two different boxes. I was almost sure that there were no interaction between two periodic images from the energy profile. In fact, the energy profile (Coul and LJ) did not show any weird behaviour. Besides this, it sounds very strange that the minimum distance goes from 3.0 nm to 0.17 nm and then up to 3.0 in 2 ps ... Therefore vmd and energy profile seem to be consistent with a proper simulation (till now ..) :) Thanks, Regards andrea Miguel Machuqueiro wrote: At 08:00 AM 6/12/2007, you wrote: Hi again, since I did not get answer I double checked my trr file. In case I calculate the minimum distance of the periodic image for each component of my complex, I get reasonable value of it (3.0 and 2.9 nm), whereas if I consider the whole system (protein) I get this strange result of 0.17 nm. Any clue? thanks again Regards Hi Andrea, When you have a multi-chain protein (or a protein + peptide) it can happen that when making protein whole (removing pbc) sometimes the two chains can be placed in two different adjacent boxes, so... when doing the g_mindist -pi setup, the closest distance is when they are together in the same box at a distance of ~1.7 Angstrom. Point 1 - This is an artifact, but it doesn't exclude the possibility that there are structures seeing their periodic images. As it was suggested by Mark Abraham, you should check these structures just to be sure. Point 2 - If someone knows how to trick trjconv -pbc in order to avoid doing this... it would be appreciated. Miguel Miguel Machuqueiro ITQB-Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Molecular Simulation Group - 6º Floor (Room 601) Av. da República, EAN, Apartado 127 2781-901 Oeiras, Portugal Tel. : +351 214469618 /Mobile: +351 96 7562285 E-mail: machuque at itqb.unl.pt _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito w w w . 5 x m i l l e . o r g ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_mindist -pi option
Just to keep the post upgraded, I have tried: trjconv -pbc nojump -o test.xtc then trjconv -fit rot+trans -f test.xtc -o test1.xtc and then run g_mindist on test1.xtc. The results of -pi is more or less the same that I obtain using vmd program. Probably it might help other people with the same problem, Regards andrea Yang Ye wrote: On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote: At 08:00 AM 6/12/2007, you wrote: Hi again, since I did not get answer I double checked my trr file. In case I calculate the minimum distance of the periodic image for each component of my complex, I get reasonable value of it (3.0 and 2.9 nm), whereas if I consider the whole system (protein) I get this strange result of 0.17 nm. Any clue? thanks again Regards Hi Andrea, When you have a multi-chain protein (or a protein + peptide) it can happen that when making protein whole (removing pbc) sometimes the two chains can be placed in two different adjacent boxes, so... when doing the g_mindist -pi setup, the closest distance is when they are together in the same box at a distance of ~1.7 Angstrom. Point 1 - This is an artifact, but it doesn't exclude the possibility that there are structures seeing their periodic images. As it was suggested by Mark Abraham, you should check these structures just to be sure. Point 2 - If someone knows how to trick trjconv -pbc in order to avoid doing this... it would be appreciated. Yes. I got such separated chain trajectory with dsDNA as well. I have a script to move them back manually frame per frame by comparing minimal distance and real distance. Miguel Miguel Machuqueiro ITQB-Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Molecular Simulation Group - 6º Floor (Room 601) Av. da República, EAN, Apartado 127 2781-901 Oeiras, Portugal Tel. : +351 214469618 /Mobile: +351 96 7562285 E-mail: machuque at itqb.unl.pt _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito w w w . 5 x m i l l e . o r g ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_mindist -pi option
Hi there, I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting periodic image of 3.0 nm, using PME and rlist=rvdw=rcoulomb=0.9. Now, I use to check the pi dist during my simulation in order to make sure that the box is larger enough. After 6ns I get this result: 03.018 4.711 6.555 6.555 6.555 30 2.791 4.514 6.557 6.557 6.557 60 2.721 4.270 6.555 6.555 6.555 90 2.762 4.378 6.554 6.554 6.554 4620 3.017 4.042 6.558 6.558 6.558 4650 0.173 9.080 6.548 6.548 6.548 4680 2.700 3.949 6.561 6.561 6.561 4710 2.881 4.113 6.560 6.560 6.560 ... 6000 2.939 4.049 6.556 6.556 6.556 So it seems that there is a spike around 4650 ps of a very low distance (quite worrying me). Any hints? is it true this value or is it pbc artefact? Thanks in advance Regards, and ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2 -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito w w w . 5 x m i l l e . o r g ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cutting out a portion of a crystal using triclinic box
I am trying to cut out a portion of a large equilbrated crystal to make a smaller crystal. I have been using the genbox command but since it tries to fill up a brick of space and my crystal is triclinic I end up will dangling molecules. Is there any command that can cut a larger configuration using a triclinic shape? I also looked at using the editconf command but it didn't actually cut out molecules. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Prot_prep_problem
HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and ligand too. However if you want to be sticked with gromos ff I do as follow: 1. prepare my system with -ignh option in pdb2gmx 2. run the simulation 3. use protonate over the pdb and the final trr in order to analyze for instance the violated NOE. Skip last question, sorry :) Regards andrea pkmukher wrote: Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output file from stage 1 using the -inter flag to get my final .top .gro and .pdb files I find that at the end of step 1 the pdb output is stripped of hydrogens. In the second stage I find that the .top file has the hydrogens listed (only polar hydrogens) but the pdb output is still without any hydrogens. I want to follow the gromacs tutorial titled GROMACS Tutorial for Drug – Enzyme Complex. http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf here they have used a prepared protein pdb file while merging the ligand coordinates to form the final complex. My questions are 1) why the pdb file written in step two does not contain the hydrogens and how can i solve this issue? 2) Is there any other way to prepare the ligand-protein complex without using the protein .pdb output? 3) This is a slightly unrelated question. Could some body guide me to any tutorials etc where they have shown how to calculate gausssian charges for the ligand and then incorporate into the gromacs ligand file? I can provide the protein structure file. I couldnt load it to the group mail because of size limitations Thanking you in anticipation Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Prot_prep_problem
I apology for the incorrect spelling of your name ... I have an automatic reply format which sometimes does weird stuff ... Sorry Prasenjit, really. Regards andrea andrea spitaleri wrote: HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and ligand too. However if you want to be sticked with gromos ff I do as follow: 1. prepare my system with -ignh option in pdb2gmx 2. run the simulation 3. use protonate over the pdb and the final trr in order to analyze for instance the violated NOE. Skip last question, sorry :) Regards andrea pkmukher wrote: Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output file from stage 1 using the -inter flag to get my final .top .gro and .pdb files I find that at the end of step 1 the pdb output is stripped of hydrogens. In the second stage I find that the .top file has the hydrogens listed (only polar hydrogens) but the pdb output is still without any hydrogens. I want to follow the gromacs tutorial titled GROMACS Tutorial for Drug – Enzyme Complex. http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf here they have used a prepared protein pdb file while merging the ligand coordinates to form the final complex. My questions are 1) why the pdb file written in step two does not contain the hydrogens and how can i solve this issue? 2) Is there any other way to prepare the ligand-protein complex without using the protein .pdb output? 3) This is a slightly unrelated question. Could some body guide me to any tutorials etc where they have shown how to calculate gausssian charges for the ligand and then incorporate into the gromacs ligand file? I can provide the protein structure file. I couldnt load it to the group mail because of size limitations Thanking you in anticipation Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] splitting of chains
Hi, if I understand well your question, you are dealing with SS bond, are you? in vmd you may not see the bond since vmd is guessing the SS bond based on the distance and not on your topology (actually the new version 1.8.5 should work better). What I think it should be important for your simulation is to check whether the SS bond is present in your topology in order to be used as it is during the gromacs simulation. Check for the specbond.dat file I hope that it helps Regards andrea özge kül wrote: After making Md simulation and getting the rmsd,gyration.. analyzing graphics I looked at the VMD.Then I saw that the 2 chains are getting splitting at a time.And then got together.So I could understand why the graphics are so bad.Then I read the manual.It says I should use -merge in pdb2gmx line if you have disulphite bridges.My molecule has 2 chains that has disulfite bonds..Anything else that you know about this except -merge? Thank you özge Don't pick lemons. See all the new 2007 cars http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE0OGRsc3F2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3Y2Fycw-- at Yahoo! Autos. http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE0OGRsc3F2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3Y2Fycw-- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ion contact: rdf does not tend to 1
Hi all, I noticed that calculating the contact between the structural ions in a protein with protein itself (the oxygen atoms actually) the rdf does tend to 0 (at 6 nm it is 0.574 but it seems going down) rather than 1. Could it be explained with the fact the I am calculating the rdf on a non-homogeneous situation?. In few words, after few nm there are not oxygen atoms interacting with the ion. Thanks Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rdf bug in 3.3.1 depending on the gcc?
Hi all, I have suspicious that g_rdf is bugged or at least it has a problem depending on the machine type. In one pc works and in another it hangs in Reading frame 0. 0.. I should also to say that in the PC not working it hangs depending on the kind of selection done, whereas in the other one it always works fine and properly. In both machine gromacs has been compiled with classic ./configure make . Version 3.3.1 PC working: gcc version 4.0.2 20050901 (prerelease) (SUSE Linux) Suse 10.0 2.6.13-15-smp PC not working: gcc version 4.1.2 20061115 (prerelease) (SUSE Linux) Suse 10.2 2.6.18.2-34-default I did not find any entry in the bugzilla. Thanks Regards, Andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] rdf bug in 3.3.1 depending on the gcc?
Hi, okay I will submit the bugzilla. Thanks Regards, andrea David van der Spoel wrote: andrea spitaleri wrote: Hi all, I have suspicious that g_rdf is bugged or at least it has a problem depending on the machine type. In one pc works and in another it hangs in Reading frame 0. 0.. I should also to say that in the PC not working it hangs depending on the kind of selection done, whereas in the other one it always works fine and properly. In both machine gromacs has been compiled with classic ./configure make . Version 3.3.1 PC working: gcc version 4.0.2 20050901 (prerelease) (SUSE Linux) Suse 10.0 2.6.13-15-smp PC not working: gcc version 4.1.2 20061115 (prerelease) (SUSE Linux) Suse 10.2 2.6.18.2-34-default I did not find any entry in the bugzilla. Thanks Regards, Andrea But there are other problems with gcc 4.1 in the mailing list, in particular analysis programs. If someone has a reproducible problem with Fedora 5 or 6 then please submit a bugzilla. -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PCoorA and Energies
Hi guys, principal coordinate analysis (PCoorA) is a variant of the classical PCA. It is the covariance matrix of the distances. Becker et al. (JCP 1998,19,1255 and 2001,114,993) sentences that the PCoorA reflects the relationship between the conformations rather than the coordinates as in the classical PCA study. In his study he reported that plotting PCoorA-1 and/or PCoorA-2 (1st and 2nd principal coordinate axis) versus the Energies one can extract a potential energy surface in order to study the different weight of the various conformers. Now, I have performed a REMD (2ns x 15 replicas) of my small peptide and I did the usual analysis on the 30ns trr trajectory. I am wondering now whether plotting the PCoorA-1/2 versus the Energies from the REMD makes physically sense, since the total energy.edr is coming from different temperatures. Any hints? any suggestions? Thanks in advance Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coordination number of ion: rdf integration
Qiao Baofu wrote:
When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr].
fine. this is clear, where rho = N/V and N = number of particles (7 ions in
this case)
and V is the total Volume.
Therefore, the efficient volume is (10x10x10). this may give you N=6.
why the efficient volume should be 10x10x10? I cannot figure out how did you
retrieve this conclusion.
Thanks for your help anyway,
Regards
Andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi (Ricerca sanitaria)
il codice fiscale della
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito
www.5xmille.org
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
