Re: [gmx-users] links warnangles
Sorry, but changing the definition and using the other suggested by Dimitris doesn't change the results, I still have the same problem in minimisation... Valerio Dimitris Dellis ha scritto: On 02/02/2011 07:47 PM, Justin A. Lemkul wrote: Dimitris Dellis wrote: Hi. There is an issue with constraints. H atom position is not uniquely defined with the constraints you use. Try these constraints (substitute symbols with numbers) 1 21 rC-H 1 31 rC-CL 1 41 rC-CL 1 51 rC-CL 2 31 rH-CL 2 41 rH-CL 3 41 rCL-CL 3 51 rCL-CL 4 51 rCL-CL I suggested this solution long ago, but Berk said it was an incorrect approach: http://redmine.gromacs.org/issues/359 In the above suggestion, the number of constraints is 9, as it should be. One constraint replaced by another in order to keep H position definition unique. Over-constraining gives wrong results. DD -Justin DD On 02/02/2011 06:20 PM, vferra...@units.it wrote: The dynamic works, but I still have the same problems with minimization... "Justin A. Lemkul" ha scritto: vferra...@units.it wrote: Ok and which definition have you used? the previous one with 5 atom for molecule? Yes. -Justin "Justin A. Lemkul" ha scritto: vferra...@units.it wrote: Just the last thing... can you copy your mdp file? I think I'm having some problems also with that... Thanks. For EM, I used the .mdp file you posted in your first message and added the line "continuation = yes." For MD, I changed nstlist from 100 to 5. -Justin Valerio "Justin A. Lemkul" ha scritto: Justin A. Lemkul wrote: I've obtained a stable trajectory for a single CHCL3 molecule. By setting "continuation = no" (so that constraints are not solved before step 0) in the em.mdp file, and then reducing nstlist to 5 in md.mdp, I Ack, this should be "continuation = yes." Sorry for the confusion. I will copy from my .mdp file...I will copy from my .mdp file... :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- 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.groma
Re: [gmx-users] protein+ligand+membrane: which forcefield?
Dear Anna, I think it's better to keep one single force field... I don't know which ff is better for your simulation, but for example you can manually correct the definition that PRODRG gives you and adjusting it for GROMOS 53a6 paramenters. Valerio anna.marabo...@isa.cnr.it ha scritto: Dear all, I have to perform a simulation in which a protein with a ligand is included in a lipid bilayer+water. In the Justin Lemkul's tutorial on membrane simulations, I see that the chosen forcefield is Gromos96 53a6 manually corrected to include the Berger lipids parameters. However, to create the topology of the ligand, I usually use PRODRG that produces the topology and parameters using the Gromos96 43a1 forcefield (it should do, at least...I see that the web server has recently changed and I don't see the indication of the forcefield used inside...) My question is: how to deal with the two different forcefields? I see in the gmx-user list that the use of different forcefields is strongly discouraged (and I agree with this suggestion) however if I have to manage such different systems, what can I do? Can I add the Berger lipids parameters to Gromos96 43a1 and use this corrected forcefield instead? I did not understand if the Gromos 53a6 ff was chosen in the tutorial because it is better than 43a1 to manage such systems, or because it is more compliant than 43a1 with Berger lipids parameters. Many thanks for suggestions and best regards. Anna Marabotti -- 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 This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to add hydrogen ions
Dear Gromacs Users, I would like to replace some of my water molecules with H+ ions, or add hydrogen ions to my water box. Please could you advice me how to do it? Yours sincerely, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to add hydrogen ions
On 3/02/2011 9:18 PM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to replace some of my water molecules with H+ ions, or add hydrogen ions to my water box. Please could you advice me how to do it? I'm not aware of any force field that implements hydrogen cation (because it is unphysical) or hydronium cation (because it would immediately take you to an impossible pH, and also not be a sound model of hydrogen transfer in real water). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to add hydrogen ions
Mark Abraham skrev 2011-02-03 11.59: On 3/02/2011 9:18 PM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to replace some of my water molecules with H+ ions, or add hydrogen ions to my water box. Please could you advice me how to do it? I'm not aware of any force field that implements hydrogen cation (because it is unphysical) or hydronium cation (because it would immediately take you to an impossible pH, and also not be a sound model of hydrogen transfer in real water). Mark There are several articles out there where an excess hydronium in water has been simulated. See e.g. the work of Lill and Holms, or Schmitt and Voth. Regards, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to add hydrogen ions
Thank you for your reply. I am not planning to simulate proton transfer in gromacs. Just it could be nice to see possible interaction. best, Olga 2011/2/3 Erik Marklund > Mark Abraham skrev 2011-02-03 11.59: > > On 3/02/2011 9:18 PM, Olga Ivchenko wrote: >> >>> Dear Gromacs Users, >>> >>> I would like to replace some of my water molecules with H+ ions, or add >>> hydrogen ions to my water box. Please could you advice me how to do it? >>> >> >> I'm not aware of any force field that implements hydrogen cation (because >> it is unphysical) or hydronium cation (because it would immediately take you >> to an impossible pH, and also not be a sound model of hydrogen transfer in >> real water). >> >> Mark >> > There are several articles out there where an excess hydronium in water has > been simulated. See e.g. the work of Lill and Holms, or Schmitt and Voth. > > Regards, > > -- > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 4537fax: +46 18 511 755 > er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ > > > -- > 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] protein+ligand+membrane: which forcefield?
Dear Justin, thank you very much for your always useful suggestions. I think I will use the combination of G43a1+Berger in order to overcome the problems of using 3 different forcefields, and I will check carefully the topology created by PRODRG for the ligand, according to your paper. Many thanks also to Valerio for his kind suggestion. Anna -- Message: 5 Date: Wed, 02 Feb 2011 12:54:32 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] protein+ligand+membrane: which forcefield? To: Discussion list for GROMACS users Message-ID: <4d499a58.7000...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed anna.marabo...@isa.cnr.it wrote: > Dear all, > > I have to perform a simulation in which a protein with a ligand is > included in a lipid bilayer+water. In the Justin Lemkul's tutorial on > membrane simulations, I see that the chosen forcefield is Gromos96 53a6 > manually corrected to include the Berger lipids parameters. However, to > create the topology of the ligand, I usually use PRODRG that produces > the topology and parameters using the Gromos96 43a1 forcefield (it > should do, at least...I see that the web server has recently changed and > I don't see the indication of the forcefield used inside...) My The original PRODRG produced topologies designed for use with Gromos87, but PRODRG beta includes 43A1: http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta Of course, neither is particularly accurate (see the linked paper): http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips > question is: how to deal with the two different forcefields? I see in > the gmx-user list that the use of different forcefields is strongly > discouraged (and I agree with this suggestion) however if I have to > manage such different systems, what can I do? Can I add the Berger > lipids parameters to Gromos96 43a1 and use this corrected forcefield > instead? I did not understand if the Gromos 53a6 ff was chosen in the > tutorial because it is better than 43a1 to manage such systems, or > because it is more compliant than 43a1 with Berger lipids parameters. > I have seen both 43A1 and 53A6 used in conjunction with the Berger lipids, and there is no fundamental difference between the two with respect to membrane protein systems. In fact, Berger + Gromos96 is, in and of itself, a compilation of different force fields. It just happens that they play nicely with one another :) I use 53A6 because it is newer and its derivation is published. The information for 43A1 is not freely available (i.e., the GROMOS software manual), so I can't decide if I like it or not. Thus, I generally do not use it. As for your problem, since the PRODRG charges and charge groups are always incorrect (at least, I've never found a molecule it builds properly), you can replace them with whatever you choose. Since the atom types (for most atoms) are named the same between 43A1 and 53A6, and the bonded parameters are the same, you can simply replace all of the charges and charge groups in the PRODRG topology and you will have a 53A6-compatible topology. Of course, that implies you've derived those charges properly, which is no small task. -Justin > Many thanks for suggestions and best regards. > > Anna Marabotti -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 82, Issue 27 * -- 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] water segment in the z-direction
Dear Tusar:
Let's keep this on the mailing list.
You could learn about expr with a simple google search! It should have
worked though, did you mangle the command somehow when you typed it?
There should be " > not_last_line.gro" with a redirect at the end but
you have only a star. Nevertheless, my scripting has improved a bit
since I wrote that and you could replace 7 by:
head -n -1 initial.gro > not_last_line.gro
And, to answer your second question, you use keep_these_waters.gro in
part 8, along with other files, to create new_system.gro
Chris.
-- original message --
I am trying to increase the size of the water segment in the z-direction.
For this purpose I am following your recommended steps and the script.
1. run genbox on initial.gro to create solvated.gro
2. cp solvated.gro new_waters.gro
3. use vi to remove everything in new_waters.gro except the new waters (make
sure you remove waters that were in initial.gro)
4. use vi to edit keepbyz.pl
- upperz and lowerz variables as you please
- sol to the name of your solvent molecule
5. run keepbyz.pl on new_waters.gro
./keepbyz new_waters.gro > keep_these_waters.gro
6. tail -1 initial.gro > last_line.gro
7. head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 )
initial.gro
* not_last_line.gro
*8. cat not_last_line.gro new_waters.gro last_line.gro >
new_system.gro 9. editconf -f new_system.gro -o
new_system_sequential_numbers.gro
I could successfully go through steps 1 to 6. However, I am unable to
execute step 7. In particular, what is "expr" in step7? Moreover, The file,
"
keep_these_waters.gro" that I have generated in step 5, where do I use
it subsequently?
I shall remain obliged for your kind answer.
Best Regards.
--
Dr. Tusar Bandyopadhyay
Theoretical Chemistry Section,
Chemistry Group
BARC, Trombay
--
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[gmx-users] solvent change-reg.
Dear GMX-users, I am not able to run the GMX molecular dynamics simulation of proteins in DMSO solvent. It is not accepting the DMSO solvent and gives error. I would be happy if GMX users help in running for solvents other than water. with thanks ***+ Dr.Karunakaran Chandran+ Biophysics Department + Medical College of Wisconsin + Milwaukee, WI-53226+ Resi.: 414-443-0085+ Off : 414-456-4034+ --- On Thu, 3/2/11, gmx-users-requ...@gromacs.org wrote: From: gmx-users-requ...@gromacs.org Subject: gmx-users Digest, Vol 82, Issue 29 To: gmx-users@gromacs.org Date: Thursday, 3 February, 2011, 5:43 AM Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: mdrun with append option (Sai Pooja) 2. Re: mdrun with append option (Sai Pooja) -- Message: 1 Date: Wed, 2 Feb 2011 18:49:28 -0500 From: Sai Pooja Subject: Re: [gmx-users] mdrun with append option To: jalem...@vt.edu, Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="iso-8859-1" Thanks Justin for being so patient. I have understood almost everything and I hope this is the last question on this thread. See inline ... On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > > On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham > mark.abra...@anu.edu.au>> wrote: >> >> On 3/02/2011 6:15 AM, Sai Pooja wrote: >> >> The problem is solved with grompp i.e. I use the -t .cpt option. >> However, now appending does not work. I remember Mark said in a >> previous mail that a certain environment variable can allow >> appending to happen even in such cases. I would liek to try that >> out. >> >> No, I said that an environment variable can override the mechanism >> that blocks ensemble changes in mdrun. >> >> So how can I use this environment variable.. I might be asking an absurd >> question since I don't really understand what an environment variable is. >> But I would definitely liek to experiment with it, since I am in the process >> of trying out these different options and figuring out which would be the >> best. >> >> > > http://en.wikipedia.org/wiki/Environment_variable > > I think the pertinent one in this case is GMX_ALLOW_CPT_MISMATCH. There is > a reason these aren't well-documented; they probably shouldn't be used in > most cases. You should have seen a very specific error message in your .log > file or screen output indicating that this situation was relevant > (src/gmxlib/checkpoint.c, around line 1606). > > > I also need to understand something. What exactly does the tpbconv do when >> only -s and -nsteps or -extend options are supplied - it seems that it takes >> all the information(mass, topology, restraints) from the previous tpr file >> and just changes the init_step parameter and the number of steps till which >> the simulation should run. >> >> > > All it does is modify the number of steps specified in the input file; > init_step should be untouched. The step from which the simulation is > continued is in the .cpt file. > > > Now if that is the case, I am still unable to understand that if the cpt >> file is NOT provided to mdrun (or a mismatched one is provided), how does >> mdrun obtain the coordinates, velocities, box-dimensions of the last frame. >> If it doesn't use the ones of the last frame, what does it really use? >> >> > > These are two cases. If (1) an invalid .cpt file is provided, the > simulation should stop with a fatal error (in checkpoint.c, described > above); if (2) a checkpoint is not provided at all, then a completely new > simulation is started, and the "last frame" is non-existent. The simulation > begins at time zero. > > > If it gets them from the new_tpr file, and the new_tpr file gets it from >> previous_tpr file via tpbconv, then how does that ensure continuation from >> the last frame, because the previous_tpr file might have been compiled even >> before the simulation started. And as far as I know, it is purely an input >> file to mdrun and has no information on the last coordinates/velocities of >> the mdrun. >> > > If you provide a .tpr file to mdrun and the checkpoint file is invalid, the > simulation should have stopped, per the fatal error given in checkpoint.c > (described above). The contents of your .log file should make clear exactly > what mdrun is doing and
Re: [gmx-users] solvent change-reg.
chandran karunakaran wrote: Dear GMX-users, I am not able to run the GMX molecular dynamics simulation of proteins in DMSO solvent. It is not accepting the DMSO solvent and gives error. I would be happy if GMX users help in running for solvents other than water. Please do not append the entire digest to your messages; it confuses the archive. Without knowing what the error was (which program? what command did you give? what have you done to prepare the solvent box?) there is nothing anyone can do to help you besides suggesting this generic information: http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation -Justin with thanks ***+ Dr.Karunakaran Chandran + Biophysics Department + Medical College of Wisconsin + Milwaukee, WI-53226 + Resi.: 414-443-0085 + Off : 414-456-4034 + -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy calculation problem with molecule leaving the box
I'm doing molecule dynamics of a calixarene in a acetonitrile box with pbc, energy groups defined and npT constant. When I extract interaction energies with g_energy from edr file I expect them to be pretty much constant because I see no significant conformational changes or changes in distance between energy groups and that is true for one part of simulation when the molecule is completely in the box. But when a molecule partially leaves the box energies of interaction for that part which is out of the is box is not calculated (bonded or with other energy groups) and interaction energy sometimes drops to 0.000 for a period of time even though the distance between groups doesn't change. I tried extracting energies through rerunning simulation on trajectories which were converted with -pbc nojump or -pbc mol -center but that gave zero energies all the time. How can I fix this energy calculation problem? -- Gordan Horvat Laboratory of Physical Chemistry Department of Chemistry Faculty of Science, University of Zagreb Horvatovac 102a 1 Zagreb Croatia phone: +385-1-4606138 fax: +385-1-4606131 -- 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] Normal modes are not orthogonal???
Hi, I am trying to understand normal mode analysis in gromacs. I just took one amino acid(Glycine), energy minimized then calculated normal mode eigenvectors as described in Gromacs manual(grompp,mdrun,g_nmeig). Then I calculated the inner product between them using 'g_anaeig'. example: g_anaeig -v eigenvec.trr -v2 eigenvec.trr -inpr I would expect all diagonal elements are 1 and the off-diagonal elements are zero. But I didn't get that. Could anyone explain to me what went wrong? PS: I did everything in double precision Thanks in advance.. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal modes are not orthogonal???
On 2011-02-03 16.41, Kumaran Baskaran wrote: Hi, I am trying to understand normal mode analysis in gromacs. I just took one amino acid(Glycine), energy minimized then calculated normal mode eigenvectors as described in Gromacs manual(grompp,mdrun,g_nmeig). Then I calculated the inner product between them using 'g_anaeig'. example: g_anaeig -v eigenvec.trr -v2 eigenvec.trr -inpr I would expect all diagonal elements are 1 and the off-diagonal elements are zero. But I didn't get that. Could anyone explain to me what went wrong? PS: I did everything in double precision How far off is it? Thanks in advance.. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Nonequilibrium MD- implementing a temperature gradient simulation
My aim is to establish a temperature gradient in the MD simulation box. I'm simulating a magnesium silicate system with interatomic potentials (Mg-Mg, Mg-Si, etc.) and no bond or angle potentials. My algorithm: 1. Divide the MD box in 12 slabs along the x-axis. 2. Pick slab 3 as my source and slab 9 as sink. 3. Find the atom with highest kinetic energy in slab 3 and the atom with lowest KE in slab 9 (I amke sure both atoms have same type and hence same mass) 4. Exchange their velocity vectors. I achieve this by making following changes to the update.c routine: **In static void do_update_md( *I comment out the position update line. v[n][d]= vb; /*xprime[n][d] = x[n][d]+vb*dt;*/ *then I exchange velocities as mentioned above *and now I update the positions based on these new velocities: xprime[n][d] = x[n][d]+v[n][d]*dt; --- I print out the kinetic energy of atoms before and after exchanging and see no problem there. Total KE of these two atoms is the same before and after. But, over the length of my simulation I see average temperature of the system keeps on increasing in the NVE ensemble-- in 1ns temperature of the system increased from 3000K -> 3500K. Note that the average temperature does not increase in the equilibrium NVE with same '.mdp' parameters (no velocity exchange). Any thoughts? Thanks, Gaurav -- 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] Adding modified nucleotide to a forcefield
Hello, I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the amber99sb force field. This is a simple modification of the H8 hydrogen on a guanine to an oxygen atom. I have followed the instructions on the gromacs site on adding residues. However the new nucleotide will not work, it will not attach to the adjacent nucleotides in the sequence. Any help would be very much appreciated, if any more information is required please let me know. Best Regards William StebbedsCranfield UniversityUK -- 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] Adding modified nucleotide to a forcefield
william Stebbeds wrote: Hello, I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the amber99sb force field. This is a simple modification of the H8 hydrogen on a guanine to an oxygen atom. I have followed the instructions on the gromacs site on adding residues. However the new nucleotide will not work, it will not attach to the adjacent nucleotides in the sequence. So a bond is missing? Any help would be very much appreciated, if any more information is required please let me know. A lot more information is needed, at the very least, your .rtp entry. -Justin Best Regards William Stebbeds Cranfield University UK -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] High Temperature simulations
Hi, Is it possible to run simulations at high temperatures? Is there any concern in dealing with the solvent water molecules when running high temperature simulations? Best, Simon Sham -- 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] High Temperature simulations
simon sham wrote: Hi, Is it possible to run simulations at high temperatures? Just about anything is possible ;) Is there any concern in dealing with the solvent water molecules when running high temperature simulations? Yes, but presumably if you have a system with a reasonable density then you can use NVT to prevent wild changes in density. There are plenty of other methodological concerns, of course (time step, validity of force field parameters, etc). There is plenty of literature on this topic, so you should start by doing some homework regarding what other people do and how you might apply it. -Justin Best, Simon Sham -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] view the vibrational modes
Hi gmx-users, Is there is any software available to view the vibrational modes selectively for particular wave number from the trajectory file. Thanks and regards, Rama -- 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] view the vibrational modes
On 4/02/2011 10:16 AM, Ramachandran G wrote: Hi gmx-users, Is there is any software available to view the vibrational modes selectively for particular wave number from the trajectory file. This is something that quantum chemists do a lot of, so I'm sure GaussView and Spartan can do it. File formatting might be a problem, however. Doubtless there is other software - Google probably knows. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Adding modified nucleotide to a forcefield
Thanks for the reply, ffamber99sb.rtp entry: [ DGO ] [ atoms ] Pamber99_461.16590 1 O1Pamber99_45 -0.77610 2 O2Pamber99_45 -0.77610 3 O5'amber99_44 -0.49540 4 C5'amber99_11 -0.00690 5 H5'1amber99_190.07540 6 H5'2amber99_190.07540 7 C4'amber99_110.16290 8 H4'amber99_190.11760 9 O4'amber99_44 -0.3691010 C1'amber99_110.0358011 H1'amber99_200.1746012 N9amber99_400.0577013 C8amber99_6 0.0736014 O8amber99_44 -0.3691015 N7amber99_36 -0.5725016 C5amber99_4 0.1991017 C6amber99_2 0.4918018 O6amber99_41 -0.5699019 N1amber99_35 -0.5053020 H1amber99_170.3520021 C2amber99_3 0.7432022 N2amber99_38 -0.9230023 H21amber99_170.4235024 H22amber99_170.4235025 N3amber99_37 -0.6636026 C4amber99_4 0.1814027 C3'amber99_110.0713028 H3'amber99_190.0985029 C2'amber99_11 -0.0854030 H2'1amber99_180.0718031 H2'2amber99_180.0718032 O3'amber99_44 -0.5232033 [ bonds ] P O1P P O2P P O5' O5' C5' C5' H5'1 C5' H5'2 C5' C4' C4' H4' C4' O4' C4' C3' O4' C1' C1' H1' C1'N9 C1' C2' N9C8 N9C4 C8O8 C8N7 N7C5 C5C6 C5C4 C6O6 C6N1 N1H1 N1C2 C2N2 C2N3 N2 H21 N2 H22 N3C4 C3' H3' C3' C2' C3' O3' C2' H2'1 C2' H2'2 -O3' P [ dihedrals ] O4' C1' N9 C4 proper_X_CT_N*_X C1' N9 C8 O8 proper_X_CK_N*_X C1' N9 C8 N7 proper_X_CK_N*_X C1' N9 C4 C5 proper_X_CB_N*_X C1' N9 C4 N3 proper_X_CB_N*_X H1' C1' N9 C8 proper_X_CT_N*_X H1' C1' N9 C4 proper_X_CT_N*_X C8 N9 C4 C5 proper_X_CB_N*_X C8 N9 C4 N3 proper_X_CB_N*_X C5 C6 N1 H1 proper_X_C_NA_X C5 C6 N1 C2 proper_X_C_NA_X C6 N1 C2 N2 proper_X_CA_NA_X C6 N1 C2 N3 proper_X_CA_NA_X O6 C6 N1 H1 proper_X_C_NA_X O6 C6 N1 C2 proper_X_C_NA_X N1 C2 N3 C4 proper_X_CA_NC_X H1 N1 C2 N2 proper_X_CA_NA_X H1 N1 C2 N3 proper_X_CA_NA_X N2 C2 N3 C4 proper_X_CA_NC_X H8 C8 N7 C5 proper_X_CK_NB_X N9 C8 N7 C5 proper_X_CK_NB_X H8 C8 N9 C4 proper_X_CK_N*_X N7 C8 N9 C4 proper_X_CK_N*_X O4' C1' C2' H2'1 proper_H_CT_CT_O O4' C1' C2' H2'2 proper_H_CT_CT_O O3' C3' C2' H2'1 proper_H_CT_CT_O O3' C3' C2' H2'2 proper_H_CT_CT_O [ impropers ] C4C8N9 C1' nucleic_imp_10 C5N1C6O6 C6C2N1H1 nucleic_imp_10 C2 H21N2 H22 N9N7C8O8 N2N1C2N3 nucleic_imp_11 DGO was also added to residuetypes.dat. hdb file was also updated, as was dna.rtp within amber99sb.ff. The problem is not a simple missing bond, as when the structure goes through pdb2gmx, the new nucleotide appears on the other side of the pbc, in a straight line (i.e. without form). Thanks Will > Date: Thu, 3 Feb 2011 16:07:42 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > william Stebbeds wrote: > > Hello, > > > > I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the > > amber99sb force field. This is a simple modification of the H8 hydrogen > > on a guanine to an oxygen atom. I have followed the instructions on the > > gromacs site on adding residues. > > > > However the new nucleotide will not work, it will not attach to the > > adjacent nucleotides in the sequence. > > > > So a bond is missing? > > > Any help would be very much appreciated, if any more information is > > required please let me know. > > > > A lot more information is needed, at the very least, your .rtp entry. > > -Justin > > > Best Regards > > > > William Stebbeds > > Cranfield University > > UK > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding modified nucleotide to a forcefield
On 4/02/2011 12:36 PM, william Stebbeds wrote: Thanks for the reply, ffamber99sb.rtp entry: [ DGO ] [ atoms ] Pamber99_461.16590 1 O1Pamber99_45 -0.77610 2 O2Pamber99_45 -0.77610 3 O5'amber99_44 -0.49540 4 C5'amber99_11 -0.00690 5 H5'1amber99_190.07540 6 H5'2amber99_190.07540 7 C4'amber99_110.16290 8 H4'amber99_190.11760 9 O4'amber99_44 -0.3691010 C1'amber99_110.0358011 H1'amber99_200.1746012 N9amber99_400.0577013 C8amber99_6 0.0736014 O8amber99_44 -0.3691015 N7amber99_36 -0.5725016 C5amber99_4 0.1991017 C6amber99_2 0.4918018 O6amber99_41 -0.5699019 N1amber99_35 -0.5053020 H1amber99_170.3520021 C2amber99_3 0.7432022 N2amber99_38 -0.9230023 H21amber99_170.4235024 H22amber99_170.4235025 N3amber99_37 -0.6636026 C4amber99_4 0.1814027 C3'amber99_110.0713028 H3'amber99_190.0985029 C2'amber99_11 -0.0854030 H2'1amber99_180.0718031 H2'2amber99_180.0718032 O3'amber99_44 -0.5232033 [ bonds ] P O1P P O2P P O5' O5' C5' C5' H5'1 C5' H5'2 C5' C4' C4' H4' C4' O4' C4' C3' O4' C1' C1' H1' C1'N9 C1' C2' N9C8 N9C4 C8O8 C8N7 N7C5 C5C6 C5C4 C6O6 C6N1 N1H1 N1C2 C2N2 C2N3 N2 H21 N2 H22 N3C4 C3' H3' C3' C2' C3' O3' C2' H2'1 C2' H2'2 -O3' P [ dihedrals ] O4' C1' N9 C4 proper_X_CT_N*_X C1' N9 C8 O8 proper_X_CK_N*_X C1' N9 C8 N7 proper_X_CK_N*_X C1' N9 C4 C5 proper_X_CB_N*_X C1' N9 C4 N3 proper_X_CB_N*_X H1' C1' N9 C8 proper_X_CT_N*_X H1' C1' N9 C4 proper_X_CT_N*_X C8 N9 C4 C5 proper_X_CB_N*_X C8 N9 C4 N3 proper_X_CB_N*_X C5 C6 N1 H1 proper_X_C_NA_X C5 C6 N1 C2 proper_X_C_NA_X C6 N1 C2 N2 proper_X_CA_NA_X C6 N1 C2 N3 proper_X_CA_NA_X O6 C6 N1 H1 proper_X_C_NA_X O6 C6 N1 C2 proper_X_C_NA_X N1 C2 N3 C4 proper_X_CA_NC_X H1 N1 C2 N2 proper_X_CA_NA_X H1 N1 C2 N3 proper_X_CA_NA_X N2 C2 N3 C4 proper_X_CA_NC_X H8 C8 N7 C5 proper_X_CK_NB_X N9 C8 N7 C5 proper_X_CK_NB_X H8 C8 N9 C4 proper_X_CK_N*_X N7 C8 N9 C4 proper_X_CK_N*_X O4' C1' C2' H2'1 proper_H_CT_CT_O O4' C1' C2' H2'2 proper_H_CT_CT_O O3' C3' C2' H2'1 proper_H_CT_CT_O O3' C3' C2' H2'2 proper_H_CT_CT_O [ impropers ] C4C8N9 C1' nucleic_imp_10 C5N1C6O6 C6C2N1H1 nucleic_imp_10 C2 H21N2 H22 N9N7C8O8 N2N1C2N3 nucleic_imp_11 DGO was also added to residuetypes.dat. hdb file was also updated, as was dna.rtp within amber99sb.ff. The problem is not a simple missing bond, as when the structure goes through pdb2gmx, the new nucleotide appears on the other side of the pbc, in a straight line (i.e. without form). Are you saying the coordinate file you gave to pdb2gmx has your modified residue at one location, and the coordinate file it output has it at some other location? (Because I doubt it). Please show us the sections of those coordinate files including your modified residue and a few atoms either side. Also, what is your pdb2gmx command line and for what GROMACS version? Mark Thanks Will > Date: Thu, 3 Feb 2011 16:07:42 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > william Stebbeds wrote: > > Hello, > > > > I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the > > amber99sb force field. This is a simple modification of the H8 hydrogen > > on a guanine to an oxygen atom. I have followed the instructions on the > > gromacs site on adding residues. > > > > However the new nucleotide will not work, it will not attach to the > > adjacent nucleotides in the sequence. > > > > So a bond is missing? > > > Any help would be very much appreciated, if any more information is > > required please let me know. > > > > A lot more information is needed, at the very least, your .rtp entry. > > -Justin > > > Best Regards > > > > William Stebbeds > > Cranfield University > > UK > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users
Re: [gmx-users] Adding modified nucleotide to a forcefield
william Stebbeds wrote: Thanks for the reply, ffamber99sb.rtp entry: [ DGO ] [ atoms ] Pamber99_461.16590 1 O1Pamber99_45 -0.77610 2 O2Pamber99_45 -0.77610 3 O5'amber99_44 -0.49540 4 C5'amber99_11 -0.00690 5 H5'1amber99_190.07540 6 H5'2amber99_190.07540 7 C4'amber99_110.16290 8 H4'amber99_190.11760 9 O4'amber99_44 -0.3691010 C1'amber99_110.0358011 H1'amber99_200.1746012 N9amber99_400.0577013 C8amber99_6 0.0736014 O8amber99_44 -0.3691015 N7amber99_36 -0.5725016 C5amber99_4 0.1991017 C6amber99_2 0.4918018 O6amber99_41 -0.5699019 N1amber99_35 -0.5053020 H1amber99_170.3520021 C2amber99_3 0.7432022 N2amber99_38 -0.9230023 H21amber99_170.4235024 H22amber99_170.4235025 N3amber99_37 -0.6636026 C4amber99_4 0.1814027 C3'amber99_110.0713028 H3'amber99_190.0985029 C2'amber99_11 -0.0854030 H2'1amber99_180.0718031 H2'2amber99_180.0718032 O3'amber99_44 -0.5232033 [ bonds ] P O1P P O2P P O5' O5' C5' C5' H5'1 C5' H5'2 C5' C4' C4' H4' C4' O4' C4' C3' O4' C1' C1' H1' C1'N9 C1' C2' N9C8 N9C4 C8O8 C8N7 N7C5 C5C6 C5C4 C6O6 C6N1 N1H1 N1C2 C2N2 C2N3 N2 H21 N2 H22 N3C4 C3' H3' C3' C2' C3' O3' C2' H2'1 C2' H2'2 -O3' P [ dihedrals ] O4' C1' N9 C4 proper_X_CT_N*_X C1' N9 C8 O8 proper_X_CK_N*_X C1' N9 C8 N7 proper_X_CK_N*_X C1' N9 C4 C5 proper_X_CB_N*_X C1' N9 C4 N3 proper_X_CB_N*_X H1' C1' N9 C8 proper_X_CT_N*_X H1' C1' N9 C4 proper_X_CT_N*_X C8 N9 C4 C5 proper_X_CB_N*_X C8 N9 C4 N3 proper_X_CB_N*_X C5 C6 N1 H1 proper_X_C_NA_X C5 C6 N1 C2 proper_X_C_NA_X C6 N1 C2 N2 proper_X_CA_NA_X C6 N1 C2 N3 proper_X_CA_NA_X O6 C6 N1 H1 proper_X_C_NA_X O6 C6 N1 C2 proper_X_C_NA_X N1 C2 N3 C4 proper_X_CA_NC_X H1 N1 C2 N2 proper_X_CA_NA_X H1 N1 C2 N3 proper_X_CA_NA_X N2 C2 N3 C4 proper_X_CA_NC_X H8 C8 N7 C5 proper_X_CK_NB_X N9 C8 N7 C5 proper_X_CK_NB_X H8 C8 N9 C4 proper_X_CK_N*_X N7 C8 N9 C4 proper_X_CK_N*_X O4' C1' C2' H2'1 proper_H_CT_CT_O O4' C1' C2' H2'2 proper_H_CT_CT_O O3' C3' C2' H2'1 proper_H_CT_CT_O O3' C3' C2' H2'2 proper_H_CT_CT_O [ impropers ] C4C8N9 C1' nucleic_imp_10 C5N1C6O6 C6C2N1H1 nucleic_imp_10 C2 H21N2 H22 N9N7C8O8 N2N1C2N3 nucleic_imp_11 DGO was also added to residuetypes.dat. hdb file was also updated, as was dna.rtp within amber99sb.ff. The problem is not a simple missing bond, as when the structure goes through pdb2gmx, the new nucleotide appears on the other side of the pbc, in a straight line (i.e. without form). As in, the atoms of DGO are visually a straight line? That would be a consequence of an incorrectly-formatted input file. If you're using a .pdb file, it's fixed-format, so any incorrect spacing will screw up the coordinates. To clarify, are you missing a bond, as your first message would imply? I can see how you might be missing bonds; your residue definition doesn't specify a bond to the next nucleotide (i.e. "O3' +P"), although if it's a 3' ending nucleotide, this wouldn't apply. If it's an internal residue, you may also be missing necessary dihedral definitions as well. -Justin Thanks Will > Date: Thu, 3 Feb 2011 16:07:42 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > william Stebbeds wrote: > > Hello, > > > > I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the > > amber99sb force field. This is a simple modification of the H8 hydrogen > > on a guanine to an oxygen atom. I have followed the instructions on the > > gromacs site on adding residues. > > > > However the new nucleotide will not work, it will not attach to the > > adjacent nucleotides in the sequence. > > > > So a bond is missing? > > > Any help would be very much appreciated, if any more information is > > required please let me know. > > > > A lot more information is needed, at the very least, your .rtp entry. > > -Justin > > > Best Regards > > > > William Stebbeds > > Cranfield University > > UK > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar
RE: [gmx-users] Adding modified nucleotide to a forcefield
Thanks again, You were right, it was a misaligned pdb file :). However I now get an error when I use grompp: ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]: No default Bond types ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]: No default Angle types ERROR 3 [file newoxi.noNaCl_DNA.itp, line 4464]: No default Angle types ERROR 4 [file newoxi.noNaCl_DNA.itp, line 6919]: No default Improper Dih. types My assumption is that I have not set the angles and dihedrals properly but have rechecked the rtp entry and all seems to be correct. Once Again thank you for helping out a gromacs newbie. > Date: Thu, 3 Feb 2011 20:43:24 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > william Stebbeds wrote: > > Thanks for the reply, > > > > ffamber99sb.rtp entry: > > [ DGO ] > > [ atoms ] > > Pamber99_461.16590 1 > >O1Pamber99_45 -0.77610 2 > >O2Pamber99_45 -0.77610 3 > >O5'amber99_44 -0.49540 4 > >C5'amber99_11 -0.00690 5 > > H5'1amber99_190.07540 6 > > H5'2amber99_190.07540 7 > >C4'amber99_110.16290 8 > >H4'amber99_190.11760 9 > >O4'amber99_44 -0.3691010 > >C1'amber99_110.0358011 > >H1'amber99_200.1746012 > > N9amber99_400.0577013 > > C8amber99_6 0.0736014 > > O8amber99_44 -0.3691015 > > N7amber99_36 -0.5725016 > > C5amber99_4 0.1991017 > > C6amber99_2 0.4918018 > > O6amber99_41 -0.5699019 > > N1amber99_35 -0.5053020 > > H1amber99_170.3520021 > > C2amber99_3 0.7432022 > > N2amber99_38 -0.9230023 > >H21amber99_170.4235024 > >H22amber99_170.4235025 > > N3amber99_37 -0.6636026 > > C4amber99_4 0.1814027 > >C3'amber99_110.0713028 > >H3'amber99_190.0985029 > >C2'amber99_11 -0.0854030 > > H2'1amber99_180.0718031 > > H2'2amber99_180.0718032 > >O3'amber99_44 -0.5232033 > > [ bonds ] > > P O1P > > P O2P > > P O5' > >O5' C5' > >C5' H5'1 > >C5' H5'2 > >C5' C4' > >C4' H4' > >C4' O4' > >C4' C3' > >O4' C1' > >C1' H1' > >C1'N9 > >C1' C2' > > N9C8 > > N9C4 > > C8O8 > > C8N7 > > N7C5 > > C5C6 > > C5C4 > > C6O6 > > C6N1 > > N1H1 > > N1C2 > > C2N2 > > C2N3 > > N2 H21 > > N2 H22 > > N3C4 > >C3' H3' > >C3' C2' > >C3' O3' > >C2' H2'1 > >C2' H2'2 > > -O3' P > > [ dihedrals ] > >O4' C1' N9 C4 proper_X_CT_N*_X > >C1' N9 C8 O8 proper_X_CK_N*_X > >C1' N9 C8 N7 proper_X_CK_N*_X > >C1' N9 C4 C5 proper_X_CB_N*_X > >C1' N9 C4 N3 proper_X_CB_N*_X > >H1' C1' N9 C8 proper_X_CT_N*_X > >H1' C1' N9 C4 proper_X_CT_N*_X > >C8 N9 C4 C5 proper_X_CB_N*_X > >C8 N9 C4 N3 proper_X_CB_N*_X > >C5 C6 N1 H1 proper_X_C_NA_X > >C5 C6 N1 C2 proper_X_C_NA_X > >C6 N1 C2 N2 proper_X_CA_NA_X > >C6 N1 C2 N3 proper_X_CA_NA_X > >O6 C6 N1 H1 proper_X_C_NA_X > >O6 C6 N1 C2 proper_X_C_NA_X > >N1 C2 N3 C4 proper_X_CA_NC_X > >H1 N1 C2 N2 proper_X_CA_NA_X > >H1 N1 C2 N3 proper_X_CA_NA_X > >N2 C2 N3 C4 proper_X_CA_NC_X > >H8 C8 N7 C5 proper_X_CK_NB_X > >N9 C8 N7 C5 proper_X_CK_NB_X > >H8 C8 N9 C4 proper_X_CK_N*_X > >N7 C8 N9 C4 proper_X_CK_N*_X > >O4' C1' C2' H2'1 proper_H_CT_CT_O > >O4' C1' C2' H2'2 proper_H_CT_CT_O > >O3' C3' C2' H2'1 proper_H_CT_CT_O > >O3' C3' C2' H2'2 proper_H_CT_CT_O > > [ impropers ] > > C4C8N9 C1' nucleic_imp_10 > > C5N1C6O6 > > C6C2N1H1 nucleic_imp_10 > > C2 H21N2 H22 > > N9N7C8O8 > > N2N1C2N3 nucleic_imp_11 > > > > DGO was also added to residuetypes.dat. hdb file was also updated, as > > was dna.rtp within amber99sb.ff. > > > > The problem is not a simple missing bond, as when the structure goes > > through pdb2gmx, the new nucleotide appears on the other side of the > > pbc, in a straight line (i.e. without form). > > > > As in, the atoms of DGO are visually a straight line? That would be a > consequence of an incorrectly-formatted input file. If you're using a .pdb > file, it's fixed-format, so any incorrect spacing will screw up the > coordinates. > > To clarify, are you missing a bond, as your first message would imply? I can > see how you might be missing bonds; your residue definition doesn't specify a > bond t
Re: [gmx-users] Adding modified nucleotide to a forcefield
william Stebbeds wrote: Thanks again, You were right, it was a misaligned pdb file :). However I now get an error when I use grompp: ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]: No default Bond types ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]: No default Angle types ERROR 3 [file newoxi.noNaCl_DNA.itp, line 4464]: No default Angle types ERROR 4 [file newoxi.noNaCl_DNA.itp, line 6919]: No default Improper Dih. types My assumption is that I have not set the angles and dihedrals properly but have rechecked the rtp entry and all seems to be correct. The errors indicate that you've specified bonded parameters that do not exist in the force field. Look into the referenced .itp file at those lines, map back the atoms in question, and identify which terms they correspond to. If you don't find matching entries in ffbonded.itp, then either you have to derive them yourself or find suitable parameters for them. -Justin Once Again thank you for helping out a gromacs newbie. > Date: Thu, 3 Feb 2011 20:43:24 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > william Stebbeds wrote: > > Thanks for the reply, > > > > ffamber99sb.rtp entry: > > [ DGO ] > > [ atoms ] > > P amber99_46 1.16590 1 > > O1P amber99_45 -0.77610 2 > > O2P amber99_45 -0.77610 3 > > O5' amber99_44 -0.49540 4 > > C5' amber99_11 -0.00690 5 > > H5'1 amber99_19 0.07540 6 > > H5'2 amber99_19 0.07540 7 > > C4' amber99_11 0.16290 8 > > H4' amber99_19 0.11760 9 > > O4' amber99_44 -0.36910 10 > > C1' amber99_11 0.03580 11 > > H1' amber99_20 0.17460 12 > > N9 amber99_40 0.05770 13 > > C8 amber99_6 0.07360 14 > > O8 amber99_44 -0.36910 15 > > N7 amber99_36 -0.57250 16 > > C5 amber99_4 0.19910 17 > > C6 amber99_2 0.49180 18 > > O6 amber99_41 -0.56990 19 > > N1 amber99_35 -0.50530 20 > > H1 amber99_17 0.35200 21 > > C2 amber99_3 0.74320 22 > > N2 amber99_38 -0.92300 23 > > H21 amber99_17 0.42350 24 > > H22 amber99_17 0.42350 25 > > N3 amber99_37 -0.66360 26 > > C4 amber99_4 0.18140 27 > > C3' amber99_11 0.07130 28 > > H3' amber99_19 0.09850 29 > > C2' amber99_11 -0.08540 30 > > H2'1 amber99_18 0.07180 31 > > H2'2 amber99_18 0.07180 32 > > O3' amber99_44 -0.52320 33 > > [ bonds ] > > P O1P > > P O2P > > P O5' > > O5' C5' > > C5' H5'1 > > C5' H5'2 > > C5' C4' > > C4' H4' > > C4' O4' > > C4' C3' > > O4' C1' > > C1' H1' > > C1' N9 > > C1' C2' > > N9 C8 > > N9 C4 > > C8 O8 > > C8 N7 > > N7 C5 > > C5 C6 > > C5 C4 > > C6 O6 > > C6 N1 > > N1 H1 > > N1 C2 > > C2 N2 > > C2 N3 > > N2 H21 > > N2 H22 > > N3 C4 > > C3' H3' > > C3' C2' > > C3' O3' > > C2' H2'1 > > C2' H2'2 > > -O3' P > > [ dihedrals ] > > O4' C1' N9 C4 proper_X_CT_N*_X > > C1' N9 C8 O8 proper_X_CK_N*_X > > C1' N9 C8 N7 proper_X_CK_N*_X > > C1' N9 C4 C5 proper_X_CB_N*_X > > C1' N9 C4 N3 proper_X_CB_N*_X > > H1' C1' N9 C8 proper_X_CT_N*_X > > H1' C1' N9 C4 proper_X_CT_N*_X > > C8 N9 C4 C5 proper_X_CB_N*_X > > C8 N9 C4 N3 proper_X_CB_N*_X > > C5 C6 N1 H1 proper_X_C_NA_X > > C5 C6 N1 C2 proper_X_C_NA_X > > C6 N1 C2 N2 proper_X_CA_NA_X > > C6 N1 C2 N3 proper_X_CA_NA_X > > O6 C6 N1 H1 proper_X_C_NA_X > > O6 C6 N1 C2 proper_X_C_NA_X > > N1 C2 N3 C4 proper_X_CA_NC_X > > H1 N1 C2 N2 proper_X_CA_NA_X > > H1 N1 C2 N3 proper_X_CA_NA_X > > N2 C2 N3 C4 proper_X_CA_NC_X > > H8 C8 N7 C5 proper_X_CK_NB_X > > N9 C8 N7 C5 proper_X_CK_NB_X > > H8 C8 N9 C4 proper_X_CK_N*_X > > N7 C8 N9 C4 proper_X_CK_N*_X > > O4' C1' C2' H2'1 proper_H_CT_CT_O > > O4' C1' C2' H2'2 proper_H_CT_CT_O > > O3' C3' C2' H2'1 proper_H_CT_CT_O > > O3' C3' C2' H2'2 proper_H_CT_CT_O > > [ impropers ] > > C4 C8 N9 C1' nucleic_imp_10 > > C5 N1 C6 O6 > > C6 C2 N1 H1 nucleic_imp_10 > > C2 H21 N2 H22 > > N9 N7 C8 O8 > > N2 N1 C2 N3 nucleic_imp_11 > > > > DGO was also added to residuetypes.dat. hdb file was also updated, as > > was dna.rtp within amber99sb.ff. > > > > The problem is not a simple missing bond, as when the structure goes > > through pdb2gmx, the new nucleotide appears on the other side of the > > pbc, in a straight line (i.e. without form). > > > > As in, the atoms of DGO are visually a straight line? That would be a > consequence of an incorrectly-formatted input file. If you're using a .pdb > file, it's fixed-format, so any incorrect spacing will screw up the coordinates. > > To clarify, are you missing a bond, as your first message would imply? I can > see how you might be missing bonds; your residue definition doesn't specify a > bond to the next nucleotide (i.e. "O3' +P"), although if it's a 3' ending > nucleotide, this wouldn't apply. If it's an internal residue, you may also be > missing necessary dihedral definitions as well. > > -Justin > > > Thanks > > > > Will > > > > > Date: Thu, 3 Feb 2011 16:07:42 -0500 > > > From: jalem...@vt.edu > > > To: gmx-users@groma
Re: [gmx-users] Energy calculation problem with molecule leaving the box
On 4/02/2011 1:05 AM, Gordan Horvat wrote: I'm doing molecule dynamics of a calixarene in a acetonitrile box with pbc, energy groups defined and npT constant. When I extract interaction energies with g_energy from edr file I expect them to be pretty much constant because I see no significant conformational changes or changes in distance between energy groups and that is true for one part of simulation when the molecule is completely in the box. But when a molecule partially leaves the box energies of interaction for that part which is out of the is box is not calculated (bonded or with other energy groups) and interaction energy sometimes drops to 0.000 for a period of time even though the distance between groups doesn't change. I tried extracting energies through rerunning simulation on trajectories which were converted with -pbc nojump or -pbc mol -center but that gave zero energies all the time. How can I fix this energy calculation problem? So, having run your original simulation with pre-defined energy groups, starting from the mdrun output files, what commands reproduce your observations? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Adding modified nucleotide to a forcefield
Success! Following your advice, and with a few tweaks everything is running smoothly, thank you so much for your help. all the best Will > Date: Thu, 3 Feb 2011 22:44:48 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > william Stebbeds wrote: > > Thanks again, > > > > You were right, it was a misaligned pdb file :). > > > > However I now get an error when I use grompp: > > > > ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]: > > No default Bond types > > > > > > ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]: > > No default Angle types > > > > > > ERROR 3 [file newoxi.noNaCl_DNA.itp, line 4464]: > > No default Angle types > > > > > > ERROR 4 [file newoxi.noNaCl_DNA.itp, line 6919]: > > No default Improper Dih. types > > > > My assumption is that I have not set the angles and dihedrals properly > > but have rechecked the rtp entry and all seems to be correct. > > > > The errors indicate that you've specified bonded parameters that do not exist > in > the force field. Look into the referenced .itp file at those lines, map back > the atoms in question, and identify which terms they correspond to. If you > don't find matching entries in ffbonded.itp, then either you have to derive > them > yourself or find suitable parameters for them. > > -Justin > > > Once Again thank you for helping out a gromacs newbie. > > > > > > > > > Date: Thu, 3 Feb 2011 20:43:24 -0500 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > > > > > > > > > william Stebbeds wrote: > > > > Thanks for the reply, > > > > > > > > ffamber99sb.rtp entry: > > > > [ DGO ] > > > > [ atoms ] > > > > P amber99_46 1.16590 1 > > > > O1P amber99_45 -0.77610 2 > > > > O2P amber99_45 -0.77610 3 > > > > O5' amber99_44 -0.49540 4 > > > > C5' amber99_11 -0.00690 5 > > > > H5'1 amber99_19 0.07540 6 > > > > H5'2 amber99_19 0.07540 7 > > > > C4' amber99_11 0.16290 8 > > > > H4' amber99_19 0.11760 9 > > > > O4' amber99_44 -0.36910 10 > > > > C1' amber99_11 0.03580 11 > > > > H1' amber99_20 0.17460 12 > > > > N9 amber99_40 0.05770 13 > > > > C8 amber99_6 0.07360 14 > > > > O8 amber99_44 -0.36910 15 > > > > N7 amber99_36 -0.57250 16 > > > > C5 amber99_4 0.19910 17 > > > > C6 amber99_2 0.49180 18 > > > > O6 amber99_41 -0.56990 19 > > > > N1 amber99_35 -0.50530 20 > > > > H1 amber99_17 0.35200 21 > > > > C2 amber99_3 0.74320 22 > > > > N2 amber99_38 -0.92300 23 > > > > H21 amber99_17 0.42350 24 > > > > H22 amber99_17 0.42350 25 > > > > N3 amber99_37 -0.66360 26 > > > > C4 amber99_4 0.18140 27 > > > > C3' amber99_11 0.07130 28 > > > > H3' amber99_19 0.09850 29 > > > > C2' amber99_11 -0.08540 30 > > > > H2'1 amber99_18 0.07180 31 > > > > H2'2 amber99_18 0.07180 32 > > > > O3' amber99_44 -0.52320 33 > > > > [ bonds ] > > > > P O1P > > > > P O2P > > > > P O5' > > > > O5' C5' > > > > C5' H5'1 > > > > C5' H5'2 > > > > C5' C4' > > > > C4' H4' > > > > C4' O4' > > > > C4' C3' > > > > O4' C1' > > > > C1' H1' > > > > C1' N9 > > > > C1' C2' > > > > N9 C8 > > > > N9 C4 > > > > C8 O8 > > > > C8 N7 > > > > N7 C5 > > > > C5 C6 > > > > C5 C4 > > > > C6 O6 > > > > C6 N1 > > > > N1 H1 > > > > N1 C2 > > > > C2 N2 > > > > C2 N3 > > > > N2 H21 > > > > N2 H22 > > > > N3 C4 > > > > C3' H3' > > > > C3' C2' > > > > C3' O3' > > > > C2' H2'1 > > > > C2' H2'2 > > > > -O3' P > > > > [ dihedrals ] > > > > O4' C1' N9 C4 proper_X_CT_N*_X > > > > C1' N9 C8 O8 proper_X_CK_N*_X > > > > C1' N9 C8 N7 proper_X_CK_N*_X > > > > C1' N9 C4 C5 proper_X_CB_N*_X > > > > C1' N9 C4 N3 proper_X_CB_N*_X > > > > H1' C1' N9 C8 proper_X_CT_N*_X > > > > H1' C1' N9 C4 proper_X_CT_N*_X > > > > C8 N9 C4 C5 proper_X_CB_N*_X > > > > C8 N9 C4 N3 proper_X_CB_N*_X > > > > C5 C6 N1 H1 proper_X_C_NA_X > > > > C5 C6 N1 C2 proper_X_C_NA_X > > > > C6 N1 C2 N2 proper_X_CA_NA_X > > > > C6 N1 C2 N3 proper_X_CA_NA_X > > > > O6 C6 N1 H1 proper_X_C_NA_X > > > > O6 C6 N1 C2 proper_X_C_NA_X > > > > N1 C2 N3 C4 proper_X_CA_NC_X > > > > H1 N1 C2 N2 proper_X_CA_NA_X > > > > H1 N1 C2 N3 proper_X_CA_NA_X > > > > N2 C2 N3 C4 proper_X_CA_NC_X > > > > H8 C8 N7 C5 proper_X_CK_NB_X > > > > N9 C8 N7 C5 proper_X_CK_NB_X > > > > H8 C8 N9 C4 proper_X_CK_N*_X > > > > N7 C8 N9 C4 proper_X_CK_N*_X > > > > O4' C1' C2' H2'1 proper_H_CT_CT_O > > > > O4' C1' C2' H2'2 proper_H_CT_CT_O > > > > O3' C3' C2' H2'1 proper_H_CT_CT_O > > > > O3' C3' C2' H2'2 proper_H_CT_CT_O > > > > [ impropers ] > > > > C4 C8 N9 C1' nucleic_imp_10 > > > > C5 N1 C6 O6 > > > > C6 C2 N1 H1 nucleic_imp_10 > > > > C2 H21 N2 H22 > > > > N9 N7 C8 O8 > > > > N2 N1 C2 N3 nucleic_imp_11 > > > > > > > > DGO was also added to residuetypes.dat. hdb file was also updated, as > > > > was dna.rtp within amber99sb.ff. > > > > > > > > The problem is not a simple m
Re: [gmx-users] Normal modes are not orthogonal???
These are the actual values extracted from xpm image Diagonal element 0.34,0.6,0.8..(which is supposed to be 1.0) Off-diagonal elements 0.3,0.21,0.01,...(which is supposed to be zero) Additional information. 1. Maximum force at the end of energy minimization is of the order of 2.1x10^-10 (Is it sufficient? I can't go below that it says "reached machine precision") 2. Energy minimization is done using l-bfgs (cg didn't give the lowest energy I tried all three) 3. I used the .trr file from energy minimization to calculate normal modes(for double precision) 4. Just a cross check: I ran normal md in glycine, then calculated eigenvectors using covariance matrix(mdrun,g_covar then g_anaeig) and then inner product between them. This was perfect. I get a neat diagonal and all off diagonals are zero. On Thu, 2011-02-03 at 19:20 +0100, David van der Spoel wrote: > On 2011-02-03 16.41, Kumaran Baskaran wrote: > > Hi, > > I am trying to understand normal mode analysis in gromacs. I just > > took one amino acid(Glycine), energy minimized then calculated normal > > mode eigenvectors as described in Gromacs manual(grompp,mdrun,g_nmeig). > > Then I calculated the inner product between them using 'g_anaeig'. > > example: g_anaeig -v eigenvec.trr -v2 eigenvec.trr -inpr > > I would expect all diagonal elements are 1 and the off-diagonal elements > > are zero. But I didn't get that. Could anyone explain to me what went > > wrong? > > > > PS: I did everything in double precision > How far off is it? > > > > > Thanks in advance.. > > > > > > > > > > Forschungszentrum Juelich GmbH > > 52425 Juelich > > Sitz der Gesellschaft: Juelich > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher > > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > > Prof. Dr. Sebastian M. Schmidt > > > > > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
