[gmx-users] re: Acpype error
Dear Prof. Aldo Segura-Cabrera, Thanks very much for your reply. I just download the package of Acpype, and I ran ../acpype.py -i FFF.pdb to test acpype.py, but then I got the error. Amber11 and AmberTools 1.4 have been successfully installed on the computer. I have read the installation instruction, I find it is only creating a linker of acpype.py, I do not know how AmberTools works with acpype.py, I will go through it. Thanks very much for your suggestion, and still could you please help me with this error? Best wishes, Qinghua Liao-- 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] Velocity distribution
Dear gmx-users, I am currently trying to simulate a thermalized wall of coarse-grained particles. I model the wall in the framework of the bead on spring approach. The wall molecules are defined as dimers : [ moleculetype ] ; molname nrexcl ROCK1 [ atoms ] ;id typeresnr residu atomcgnrcharge 1 PRC 1 ROCKPRC 1 0 2 FRC 1 ROCKFRC 2 0 [bonds] ; i j funct lengthforce.c. 1 2 1 0.0 1000 And then the beads of one type (FRC) are defined to be fixed and no thermostat is applied to them. There are no interactions between the particles in the system (ensemble of ideal harmonic oscillators): energygrps = FRC PRC tcoupl = v-rescale tc-grps = PRC FRC tau_t= 0.5 0 ref_t= 300 0 freezegrps = FRC freezedim= Y Y Y energygrp_excl = FRC FRC FRC PRC PRC PRC The problem I have is that when I build the velocity distribution for the mobile particles (atom type PRC), the distribution does not correspond to the Maxwell's distribution (is shifted to the left). Am I missing something very basic? In my previous simulations for the same system but using another MD code with stochastic (DPD) thermostat the Maxwellian distribution was reproduced without any problem. Many thanks in advance, Mikhail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re : Simulation for prediction of binding between a peptide and protein
I suppose by full body dock you mean rigid body docking, correct me if I am wrong. In that case you could create initial starting structure for flexible peptide docking. Rosetta accepts even coarse-grained models, namely only the backbone, and then builds the full-atom structures. Alternatively you could predict potential peptide binding sites on your protein (i.e. by using this server http://pepsite.russelllab.org/index.html) and the run SMD to force the peptide to attach to these putative binding sites, and thus create initial coordinates for Rosetta. This approach is more tedious. Nevertheless, flexible peptide docking with Rosetta takes approximately 3 minutes per decoy on an average node and has sub-angstrom accuracy. Posting a question in the Rosetta forum doesn't sound like a bad idea. On 12 April 2011 03:11, bharat gupta bharat.85.m...@gmail.com wrote: but using docking I have to fix the grid and have to dock at that position... which is not my objective ... I want the peptide to come and bind own its own to the protein... I have heard of full body dock , in which there is no need to define grid points , will that be useful ?? On Mon, Apr 11, 2011 at 2:02 PM, Thomas Evangelidis teva...@gmail.comwrote: You can try Rosetta for flexible peptide docking. On 11 April 2011 15:32, Mark Abraham mark.abra...@anu.edu.au wrote: Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ?? I don't think anybody has the computational resources to answer this question with unguided MD. Docking programs are probably the way to get a guide about what binding modes might be reasonable, but I don't know what software might be fit for the purpose. 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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Acpype error
Hi Liao, Your python installation seems to be missing the datetime module, which is very bizarre. Please verify your Python installation, you may have issues with your PYTHONPATH. Regards, Alan 2011/4/12 fancy2012 fancy2...@yeah.net Hi GMX users, When I ran acpype.py on my computer, I got one error like this: File ./acpype.py, line 67, in module from datetime import datetime ImportError: No module named datetime I use Python-2.6.6, I do not know how this error happen, could someone help me figure it out? Thanks very much in advance! -- *Best wishes,* *Qinghua Liao* *Ph.D student of Tianjin University, China* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Interesting. I can't see why that wouldn't be possible in theory, but there is a part of the code that would need rewriting, however. Erik Nilesh Dhumal skrev 2011-04-12 04.11: I tried to use contact and -da together with following command g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc -noda -r 0.5 -contact -num I am getting following error. Fatal error:Can not analyze contact between H and A: turn off -noda Nilesh On Mon, April 11, 2011 5:05 pm, Nilesh Dhumal wrote: Is it possible to find number of hydrogen bonds using g_hbond by considering the distance between Acceptor-hydrogen instead of the distance between Acceptor-Donor atoms. Nilesh On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote: Try the -contact option. Erik Nilesh Dhumal skrev 2011-04-11 17.12: Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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 -- --- 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 -- --- 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] aminoacids.n.tdb
Hi Mark, Thank you for your reply. But, I couldn’t understand very well what you meant “you can make one that uses backbone-style linking. Most of the forcefields will have examples of non-amino-acid terminating residues - these make a single peptide bond just like yours does.”. So, let me explain the problem a little more. I would be happy if you could expound upon your reply. *1)* I prepared the *rtp *entry for the lauroic acid (see below) and add the lipid parameters to the relevant sections of the *ffnonbonded.itp*and *ffbonded.itp* files. *2)* I added the lauroic acid as a Non-Protein” in the * residuetypes.dat *file and also I introduced the atom types (LO: 15.9994, LC: 12.0110, LP2: 14.0270, LP3: 15.0350) in the *atomtypes.atp.* *3) *I concatenated the structure files of a 8-residue-peptide* *and lauroic acid as *system.gro. *Then, using “pdb2gmx -ter”, I obtained the *topol.top, conf.gro* and *posre.itp* for *the whole system.* (I chose : start terminus VAL-2: NH2 and end terminus ASP-9: COO-) *4)* But when I looked into *conf.gro* with the VMD, I see that the peptide bond is formed between the lauroic acid (C34) and the N terminal of the Valine. However, second H of the N is still there and it is making another bond with C34 of lauroic acid. The strange thing is: C34 is double bonded to O35, Carbon makes four bonds. How can I get rid of that H? [ DPP ] [ atoms ] C34 LC 0.80018 O35 LO-0.60 18 C36 LP2 0 19 C37 LP2 0 20 C38 LP2 0 21 C39 LP2 0 22 C40 LP2 0 23 C41 LP2 0 24 C42 LP2 0 25 C43 LP2 0 26 C44 LP2 0 27 C45 LP2 0 28 C46 LP3 0 29 [ bonds ] ; aiaj funct 34 35 1 0.12300E+00 0.50210E+06 34 36 1 0.15300E+00 0.33470E+06 36 37 1 0.15300E+00 0.33470E+06 37 38 1 0.15300E+00 0.33470E+06 38 39 1 0.15300E+00 0.33470E+06 39 40 1 0.15300E+00 0.33470E+06 40 41 1 0.15300E+00 0.33470E+06 41 42 1 0.15300E+00 0.33470E+06 42 43 1 0.15300E+00 0.33470E+06 43 44 1 0.15300E+00 0.33470E+06 44 45 1 0.15300E+00 0.33470E+06 45 46 1 0.15300E+00 0.33470E+06 [ angles ] ; aiajak funct 34 36 37 1 0.11100E+03 0.46020E+03 35 34 36 1 0.12100E+03 0.50210E+03 36 37 38 1 0.11100E+03 0.46020E+03 37 38 39 1 0.11100E+03 0.46020E+03 38 39 40 1 0.11100E+03 0.46020E+03 39 40 41 1 0.11100E+03 0.46020E+03 40 41 42 1 0.11100E+03 0.46020E+03 41 42 43 1 0.11100E+03 0.46020E+03 42 43 44 1 0.11100E+03 0.46020E+03 43 44 45 1 0.11100E+03 0.46020E+03 44 45 46 1 0.11100E+03 0.46020E+03 [ dihedrals ] ; aiajakal funct phi0 cp mult 34363738 10.0 5.863 36373839 3 37383940 3 38394041 3 39404142 3 40414243 3 41424344 3 42434445 3 43444546 3 Best regards, Deniz On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote: Hi Gromacs users, I want to covalently link the lauroic acid to the Valine residue (it is a peptide (amide) bond), I know that I should update the specbond.dat.But before updating this file, I need the NH as an N terminal of the first residue (Valine).When I used pdb2gmx with the –ter flag, I got either NH3, NH2 or None instead of NH.So, I add the [NH] directive in the aminoacids.n.rtp file, as follows; [ NH ] [ replace ] ; old-namenew-typenew-massnew-charge NLN14.0067-0.31 CACH113.0190.127 [ add ] 12HNCAC ;atom_typemasscharge H1.0080.31 [ delete ] H [ bonds ] NHgb_2 [ angles ] CANHga_11 [ dihedrals ] HNCACgd_29 (ps. I wrote the charges of N, CA and H according to values defined in topol.top and also I used the Gromos96 53a6 force field) Then, I used the pdb2gmx with –ter, I could see: Select start terminus type for VAL 0: NH 1: NH3+ 2: NH2 3: None Finally, I got thetopol.top, posre itp and conf.gro files. But when I looked into conf.gro, I see that I am getting “None”. How can I get the NH ? Coordinating multiple moving parts like the specbond and terminus-fixing is probably a recipe for trouble. Since you have to make an .rtp entry for lauroic acid anyway, you can make one that uses backbone-style linking. Most of the
[gmx-users] Unexpected results arising from T- and P-coupling methods
I can't tell you if there is a problem or not. The only intended difference that I can see is that for 4.5.X: # grompp by default sets the new nsttcouple parameter equal to nstlist, this means T-coupling is done less frequently; grompp checks if tau_t is large enough # grompp by default sets the new nstpcouple parameter equal to nstlist, this means P-coupling is done less frequently; grompp checks if tau_p is large enough (see http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x ) Note that there were some fixes to P-R scaling in the 4.0.X series -- se http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 To test this further, I suggest that you need to define a good procedure to ensure that what you are seeing is (b) from a well equilibrated system and is also (b) statistically significant. I suggest that one way to do this is to cycle through your T- and P- coupling options at a given temperature. For example, at T=500 K, run X ns of Berendsen, then X ns of Parrinello-Rahman, then back to Berendsen, and so on for a few cycles. Each time you switch coupling method, be sure to use the structure output from the previous run. Also be sure that X ns is as long as you can afford. This way, you will be able to pick out systematic changes as temperature/density oscillations with periods that are related to your changes of algorithm. This also ensures that what you are seeing is not simply an artifact of having a poorly equilibrated density in your initial structure. You could also run the same cycle with Berendsen and V-rescale. Chris. -- original message -- Dear gmxers, According to my recent practice, we find that the Berensen methods for T- and P- coupling can yield reasonable averaged density as a function of temperature, but when the v-rescale method and the Parrinello-Rahman method are employed for T- and P- coupling, somewhat unexpected results (i.e. density at higher temperature is bigger than that at lower tempearature) are obtained. Generally, the latter setup is considered to be prefered to the former one in simulating realistic ensemble. I am using gmx-4.5.3, and previously I have also performed one similar work using 4.0 which can generate expected results using the latter setup. I wonder if this version 4.5.3 has some bugs in calculating T and P, and are they dealt with in 4.5.4? Please give me some hints. Yours sincerely, Chaofu Wu, Dr. -- Department of Chemistry and Materials Science, Hunan University of Humanities, Science and Technology, Loudi 417000, the People?s Republic of China (P.R. China) -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110412/ceadf085/attachment.html -- 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] aminoacids.n.tdb
On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote: Hi Mark, Thank you for your reply. But, I couldn’t understand very well what you meant “you can make one that uses backbone-style linking. Most of the forcefields will have examples of non-amino-acid terminating residues - these make a single peptide bond just like yours does.”.So, let me explain the problem a little more.I would be happy if you could expound upon your reply. *1)*I prepared the *rtp *entry for the lauroic acid (see below) and add the lipid parameters to the relevant sections of the *ffnonbonded.itp* and *ffbonded.itp* files. That is not an .rtp entry, see below. Look at some .rtp entries and see how they make backbone bonds. That is what I understand you want to do - make a peptide bond as if lauroic acid was an amino acid. *2)*I added the lauroic acid as a Non-Protein” in the *residuetypes.dat*file and also I introduced the atom types (LO: 15.9994, LC:12.0110, LP2: 14.0270, LP3: 15.0350) in the *atomtypes.atp.* *3)*I concatenatedthe structure files of a 8-residue-peptide**and lauroic acid as *system.gro. *Then, using “pdb2gmx -ter”, I obtained the *topol.top, conf.gro* and *posre.itp* for *the whole system.* (I chose : start terminus VAL-2: NH2 and end terminus ASP-9: COO-) *4)* But when I looked into *conf.gro* with the VMD, I see that the peptide bond is formed between the No bond shown by VMD is relevant. It's guessing based on the coordinates in your .gro file. Your bonded atoms are in your .top file. VMD knows nothing about your .top file. lauroic acid (C34) and the N terminal of the Valine. However, second H of the N is still there and it is making another bond with C34 of lauroic acid. The strange thing is: C34 is double bonded to O35,Carbon makes four bonds. How can I get rid of that H? [ DPP ] This is not an .rtp entry. The [bonds] section must refer to atom names. I can only suppose pdb2gmx is warning about or ignoring everything after your [atoms] section. Look in the .rtp and chapter 5 of the manual how terminating pseudo-residues like ACE work. Do something analogous for lauroic acid. Mark [ atoms ] C34LC0.80018 O35LO-0.6018 C36LP2019 C37LP2020 C38LP2021 C39LP2022 C40LP20 23 C41LP2024 C42LP2025 C43LP2026 C44LP2027 C45LP2028 C46LP3029 [ bonds ] ;aiaj funct 34351 0.12300E+00 0.50210E+06 34361 0.15300E+00 0.33470E+06 36371 0.15300E+00 0.33470E+06 37381 0.15300E+00 0.33470E+06 38391 0.15300E+00 0.33470E+06 39401 0.15300E+00 0.33470E+06 40411 0.15300E+00 0.33470E+06 41421 0.15300E+00 0.33470E+06 42431 0.15300E+00 0.33470E+06 43441 0.15300E+00 0.33470E+06 44451 0.15300E+00 0.33470E+06 45461 0.15300E+00 0.33470E+06 [ angles ] ;aiajak funct 3436371 0.11100E+03 0.46020E+03 3534361 0.12100E+03 0.50210E+03 3637381 0.11100E+03 0.46020E+03 3738391 0.11100E+03 0.46020E+03 3839401 0.11100E+03 0.46020E+03 3940411 0.11100E+03 0.46020E+03 4041421 0.11100E+03 0.46020E+03 4142431 0.11100E+03 0.46020E+03 4243441 0.11100E+03 0.46020E+03 4344451 0.11100E+03 0.46020E+03 4445461 0.11100E+03 0.46020E+03 [ dihedrals ] ;aiajakal functphi0cpmult 3436373810.05.863 363738393 373839403 383940413 394041423 404142433 414243443 424344453 434445463 Best regards, Deniz On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote: Hi Gromacs users, I want to covalently link the lauroic acid to the Valine residue (it is a peptide (amide) bond), I know that I should update the specbond.dat.But before updating this file, I need the NH as an N terminal of the first residue (Valine).When I used pdb2gmx with the –ter flag, I got either NH3, NH2 or None instead of NH.So, I add the [NH] directive in the aminoacids.n.rtp file, as follows; [ NH ] [ replace ] ; old-namenew-typenew-massnew-charge NLN14.0067-0.31 CACH113.0190.127 [ add ] 12HNCAC ;atom_typemasscharge H1.0080.31 [ delete ] H [ bonds ] NHgb_2 [ angles ] CANHga_11 [ dihedrals ] HNCACgd_29 (ps. I wrote the charges of N, CA and H according to values defined in topol.top and also I used the Gromos96 53a6 force field) Then, I used the pdb2gmx with –ter, I could see: Select start terminus type for VAL 0: NH 1: NH3+ 2: NH2 3: None Finally, I got thetopol.top, posre itp and conf.gro files. But when I looked into conf.gro, I see that I am getting “None”. How can I get the NH ? Coordinating multiple moving parts like the specbond and terminus-fixing is probably a recipe for trouble. Since you have to make an .rtp entry for lauroic acid anyway, you can make one that
Re: [gmx-users] Unexpected results arising from T- and P-coupling methods
Hello, I have also realized similar behaviour: NpT simulations performed with a Berendsen barostat give lower densities than simulations coupled with P-R. However I think this is due to the fact that I never achieve a pressure of 1bar (it is always around 1.2bar) with P-R even after a previous equilibration of 40ns. I am aware that pressure is a strongly fluctuating quantity and this topic has been discussed for several times on the list, but the equations of motion for the box size given by the Lagrangian for P-R should finally give an average pressure of 1bar even if the fluctuations are large. So what I assume is, that the Leap-Frog integrator is not suitable for this coupling scheme, BUT THIS IS JUST AN ASSUMPTION I DO NOT KNOW, and unfortunately I had no time to try and validate this, yet. /Flo On Tue, 2011-04-12 at 09:13 -0400, chris.ne...@utoronto.ca wrote: I can't tell you if there is a problem or not. The only intended difference that I can see is that for 4.5.X: # grompp by default sets the new nsttcouple parameter equal to nstlist, this means T-coupling is done less frequently; grompp checks if tau_t is large enough # grompp by default sets the new nstpcouple parameter equal to nstlist, this means P-coupling is done less frequently; grompp checks if tau_p is large enough (see http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x ) Note that there were some fixes to P-R scaling in the 4.0.X series -- se http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 To test this further, I suggest that you need to define a good procedure to ensure that what you are seeing is (b) from a well equilibrated system and is also (b) statistically significant. I suggest that one way to do this is to cycle through your T- and P- coupling options at a given temperature. For example, at T=500 K, run X ns of Berendsen, then X ns of Parrinello-Rahman, then back to Berendsen, and so on for a few cycles. Each time you switch coupling method, be sure to use the structure output from the previous run. Also be sure that X ns is as long as you can afford. This way, you will be able to pick out systematic changes as temperature/density oscillations with periods that are related to your changes of algorithm. This also ensures that what you are seeing is not simply an artifact of having a poorly equilibrated density in your initial structure. You could also run the same cycle with Berendsen and V-rescale. Chris. -- original message -- Dear gmxers, According to my recent practice, we find that the Berensen methods for T- and P- coupling can yield reasonable averaged density as a function of temperature, but when the v-rescale method and the Parrinello-Rahman method are employed for T- and P- coupling, somewhat unexpected results (i.e. density at higher temperature is bigger than that at lower tempearature) are obtained. Generally, the latter setup is considered to be prefered to the former one in simulating realistic ensemble. I am using gmx-4.5.3, and previously I have also performed one similar work using 4.0 which can generate expected results using the latter setup. I wonder if this version 4.5.3 has some bugs in calculating T and P, and are they dealt with in 4.5.4? Please give me some hints. Yours sincerely, Chaofu Wu, Dr. -- Department of Chemistry and Materials Science, Hunan University of Humanities, Science and Technology, Loudi 417000, the People?s Republic of China (P.R. China) -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110412/ceadf085/attachment.html -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] orientational relaxation
thanks Mark and Tsjerk i got it..! --- On Mon, 4/11/11, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] orientational relaxation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, April 11, 2011, 10:54 PM Hi Daniel, If you want to fix the com position, specify the molecule as comm-grps. If you really don't want movement of the com, and use pressure coupling, first put the molecule at the origin. Hope it helps, Tsjerk On Apr 12, 2011 7:28 AM, Mark Abraham mark.abra...@anu.edu.au wrote: yes , position restraints of molecules that only allow to orient. What's your question? Most tutorials will use position restraints at some stage. There's theory discussion in the manual. Mark regards. --- On Mon, 4/11/11, Mark Abraham mark.abra...@anu.edu.au wrote: From:... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] re: Acpype error
First of all, I don't know if this is the right forum to discuss issues related to acpype. You should try to contact the acpype team. I'm not an acpype expert but if I can help you, do not hesitate to contact me through my email. Some tips: Considering that python, openbabel and Ambertools are properly installed and if the test shows an error, then something is wrong with the installation. How do you download the program? By: svn or wget if you want I can send you a copy that I use and works well, so you can try to install it. Regards, Aldo=== Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com = --- El mar 12-abr-11, fancy2012 fancy2...@yeah.net escribió: De: fancy2012 fancy2...@yeah.net Asunto: [gmx-users] re: Acpype error A: gmx-users@gromacs.org Fecha: martes, 12 de abril de 2011, 0:57 Dear Prof. Aldo Segura-Cabrera, Thanks very much for your reply. I just download the package of Acpype, and I ran ../acpype.py -i FFF.pdb to test acpype.py, but then I got the error. Amber11 and AmberTools 1.4 have been successfully installed on the computer. I have read the installation instruction, I find it is only creating a linker of acpype.py, I do not know how AmberTools works with acpype.py, I will go through it. Thanks very much for your suggestion, and still could you please help me with this error? Best wishes, Qinghua Liao -Sigue archivo adjunto- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR
Miguel Quiliano Meza wrote: Dear community. Justin was right. I did not want to make the explanation so long, but you're right I have to put those details. As you will see I had to redirect the outputs after perform *./configure* and *make* (these files are attach to this mail). I sincerely hope you can give their opinions and help. Thanks in advance. Miguel Quiliano. Here are the general procedure: root@bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz [root@bioinfocluster src]# export LDFLAGS=-L/opt/rocks/lib [root@bioinfocluster src]# export CPPFLAGS=-I/opt/rocks/include [root@bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi --prefix=/share/apps/opt/gromacs output [root@bioinfocluster gromacs-4.5.4]# make output2 mempool.c: In function '_gmx_sel_mempool_alloc_group': mempool.c:201: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c: In function '_gmx_selelem_mempool_reserve': selelem.c:203: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c:208: warning: dereferencing type-punned pointer will break strict-aliasing rules checkpoint.c: In function 'do_cpt_state': checkpoint.c:852: warning: dereferencing type-punned pointer will break strict-aliasing rules /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC This issue and its resolution are specifically described in the installation instructions: http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites (Under the a few tips heading) -Justin /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd_mpi.la http://libmd_mpi.la/] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] re: Acpype error
You should check also that you use for acpype a python installation under which the openbabel is installed. Lucio Montero Instituto de Biotecnología, UNAM. --- El mar, 12-04-2011 a las 07:29 -0700, Aldo Segura escribió: First of all, I don't know if this is the right forum to discuss issues related to acpype. You should try to contact the acpype team. I'm not an acpype expert but if I can help you, do not hesitate to contact me through my email. Some tips: Considering that python, openbabel and Ambertools are properly installed and if the test shows an error, then something is wrong with the installation. How do you download the program? By: svn or wget if you want I can send you a copy that I use and works well, so you can try to install it. Regards, Aldo === Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com = --- El mar 12-abr-11, fancy2012 fancy2...@yeah.net escribió: De: fancy2012 fancy2...@yeah.net Asunto: [gmx-users] re: Acpype error A: gmx-users@gromacs.org Fecha: martes, 12 de abril de 2011, 0:57 Dear Prof. Aldo Segura-Cabrera, Thanks very much for your reply. I just download the package of Acpype, and I ran ../acpype.py -i FFF.pdb to test acpype.py, but then I got the error. Amber11 and AmberTools 1.4 have been successfully installed on the computer. I have read the installation instruction, I find it is only creating a linker of acpype.py, I do not know how AmberTools works with acpype.py, I will go through it. Thanks very much for your suggestion, and still could you please help me with this error? Best wishes, Qinghua Liao -Sigue archivo adjunto- -- 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 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] Differences in default values for nstpcouple and cmap atomtypes between versions 4.0 and 4.5.4
Hi,
I've started using version 4.5.4 of gromacs, having previously been
using version 4.0 on an older server.
When I run a simulation on v4.0 everything seems to run fine.
However, when I run the same simulation on v4.5.4, mdrun gives me the
error message:
Making 3D domain decomposition 4 x 3 x 2
starting mdrun 'PROTEIN IN BILAYER'
500 steps, 15.0 ps.
step 0
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
.
.
.
.
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
.
.
.
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
Step 25, time 0.75 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.04, max 0.15 (between atoms 147 and 148)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
178179 34.70.2600 0.2600 0.2600
Step 28, time 0.84 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 19.241184, max 126.849724 (between atoms 35 and 36)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 28, time 0.84 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.739422, max 8.610986 (between atoms 496 and 497)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
45 46 90.00.2650 0.5083 0.2650
35 36 90.00.3100 39.6334 0.3100
42 43 90.00.2600 1.2129 0.2600
45 46 90.00.2650 0.5083 0.2650
482483 90.00.2600 0.8649 0.2600
496497 90.00.2700 2.5950 0.2700
496498 90.00.2700 1.4511 0.2700
497498 90.00.2700 2.5822 0.2700
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
I've run g_gmxdump/gmxdump to get the input parameters for the
simulations using the 2 different versions, which I can't attach
because they're too big but which differ in the lines shown below
(v4.0 on the left and v4.5.4 on the right):
nstcomm = 1 |nstcomm
= 10
nstcalcenergy= 1 |
nstcalcenergy= 10
nsttcouple = 1 |nsttcouple
= 10
nstpcouple = 1 |nstpcouple
= 10
rgbradii = 2 |rgbradii
= 1
sa_surface_tension = 2.092 | sa_surface_tension =
2.05016
sc_sigma_min = 0 |sc_sigma_min
= 0.3
nstdhdl = 1 |nstdhdl
= 10
and also for cmap atomtypes values:
in v4.0:
atomtype[ 0]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 1]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 2]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 3]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 4]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 5]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 6]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 7]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 8]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 9]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 10]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00,
[gmx-users] Saikat Banerjee wants to stay in touch on LinkedIn
LinkedIn Saikat Banerjee requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Saikat Banerjee Accept invitation from Saikat Banerjee http://www.linkedin.com/e/-85v1n9-gmf3gueh-2y/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2748024960_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnP0SejgOc3wQdP99bRFoglcPpQoTbPsUdzgUc38Udz8LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Saikat Banerjee http://www.linkedin.com/e/-85v1n9-gmf3gueh-2y/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2748024960_2/39vc3oVd38Me3gTcAALqnpPbOYWrSlI/svi/ -- Why might connecting with Saikat Banerjee be a good idea? Saikat Banerjee's connections could be useful to you: After accepting Saikat Banerjee's invitation, check Saikat Banerjee's connections to see who else you may know and who you might want an introduction to. Building these connections can create opportunities in the future. -- (c) 2011, LinkedIn Corporation-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 : ERROR
Hi everyone. I followed the steps in http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites for my problem, but I obtained problems at the moment to perform make. So, as mention the web page of gromacs... If you get errors during GROMACS compilation (the make step) that suggest that you recompile with -fPIC, then you should return to this FFTW stage and configure with --enable-shared or --with-pic. By the way, previously I performed make with FFTW version 3.2.2 (default version in rocks cluster 5.4) I did: root@bioinfocluster fftw-3.2.2]# ./configure --enable-threads --prefix=/share/apps/opt/fftw Without errors, and then: [root@bioinfocluster fftw-3.2.2]# make make[3]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' Making all in m4 make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4' make[1]: Leaving directory `/share/apps/src/fftw-3.2.2' What could be the problem? please advices. Miguel Quiliano. Miguel Quiliano Meza wrote: Dear community. Justin was right. I did not want to make the explanation so long, but you're right I have to put those details. As you will see I had to redirect the outputs after perform *./configure* and *make* (these files are attach to this mail). I sincerely hope you can give their opinions and help. Thanks in advance. Miguel Quiliano. Here are the general procedure: root@bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz [root@bioinfocluster src]# export LDFLAGS=-L/opt/rocks/lib [root@bioinfocluster src]# export CPPFLAGS=-I/opt/rocks/include [root@bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi --prefix=/share/apps/opt/gromacs output [root@bioinfocluster gromacs-4.5.4]# make output2 mempool.c: In function '_gmx_sel_mempool_alloc_group': mempool.c:201: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c: In function '_gmx_selelem_mempool_reserve': selelem.c:203: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c:208: warning: dereferencing type-punned pointer will break strict-aliasing rules checkpoint.c: In function 'do_cpt_state': checkpoint.c:852: warning: dereferencing type-punned pointer will break strict-aliasing rules /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC This issue and its resolution are specifically described in the installation instructions: http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites (Under the a few tips heading) -Justin /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd_mpi.la http://libmd_mpi.la/] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 : ERROR
Miguel Quiliano Meza wrote: Hi everyone. I followed the steps in http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites for my problem, but I obtained problems at the moment to perform make. So, as mention the web page of gromacs... If you get errors during GROMACS compilation (the make step) that suggest that you recompile with -fPIC, then you should return to this FFTW stage and configure with |--enable-shared| or |--with-pic|. By the way, previously I performed make with FFTW version 3.2.2 (default version in rocks cluster 5.4) I did: root@bioinfocluster fftw-3.2.2]# ./configure --enable-threads --prefix=/share/apps/opt/fftw Without errors, and then: [root@bioinfocluster fftw-3.2.2]# make make[3]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' Making all in m4 make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4' make[1]: Leaving directory `/share/apps/src/fftw-3.2.2' What could be the problem? please advices. There is no problem, per se, with what you did. FFTW appears to have been installed fine. However, as noted in the above quote from the Installation Instructions, you will need to re-install FFTW using one of the options listed. -Justin Miguel Quiliano. Miguel Quiliano Meza wrote: Dear community. Justin was right. I did not want to make the explanation so long, but you're right I have to put those details. As you will see I had to redirect the outputs after perform *./configure* and *make* (these files are attach to this mail). I sincerely hope you can give their opinions and help. Thanks in advance. Miguel Quiliano. Here are the general procedure: root@bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz [root@bioinfocluster src]# export LDFLAGS=-L/opt/rocks/lib [root@bioinfocluster src]# export CPPFLAGS=-I/opt/rocks/include [root@bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi --prefix=/share/apps/opt/gromacs output [root@bioinfocluster gromacs-4.5.4]# make output2 mempool.c: In function '_gmx_sel_mempool_alloc_group': mempool.c:201: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c: In function '_gmx_selelem_mempool_reserve': selelem.c:203: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c:208: warning: dereferencing type-punned pointer will break strict-aliasing rules checkpoint.c: In function 'do_cpt_state': checkpoint.c:852: warning: dereferencing type-punned pointer will break strict-aliasing rules /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC This issue and its resolution are specifically described in the installation instructions: http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites (Under the a few tips heading) -Justin /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd_mpi.la http://libmd_mpi.la http://libmd_mpi.la/] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ** -- 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] Essential Dynamics lincs warning
Hi, I am running essential dynamics for a protein in water system (charmm-nocmap and tip3p). I use the first 25 eigenvectors and targeted ED. It stops after 630ps when settle and lincs start giving warnings. Step 315573, time 631.146 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000121, max 0.003164 (between atoms 144 and 145) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 148151 36.20.1112 0. 0. 144145 45.70.1109 0.1107 0. I am also running the same simulation with the first 12 eigenvectors and face no such problems. I understand that targeted ED may lead to some unphysical trajectory which may be the cause of this error. However, is there a way to override this and in that case an alternative check which may be used instead of lincs rotation constraint to make sure that the contacts arent unphysical? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] Regarding creating interface between two solvent at particular site
Hello I am trying to build a solvent box of two solvents. Water octane. I want to create a interface at a particular site of the protein, as i am studying interfacial activation of Lipase's lid. Kindly suggest. Thanks Yuvraj -- 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] Regarding creating interface between two solvent at particular site
On 13/04/2011 7:09 AM, YUVRAJ UBOVEJA wrote: Hello I am trying to build a solvent box of two solvents. Water octane. I want to create a interface at a particular site of the protein, as i am studying interfacial activation of Lipase's lid. Kindly suggest. The mailing list archives contain several discussions of this topic. Please have a search. 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] Regarding creating interface between two solvent at particular site
Mark Abraham wrote: On 13/04/2011 7:09 AM, YUVRAJ UBOVEJA wrote: Hello I am trying to build a solvent box of two solvents. Water octane. I want to create a interface at a particular site of the protein, as i am studying interfacial activation of Lipase's lid. Kindly suggest. The mailing list archives contain several discussions of this topic. Please have a search. There's even a tutorial: http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR
Please make sure to keep all discussion on the list. Miguel Quiliano Meza wrote: Hi Justin. Unfortunately, the problem persist. So... for the moment I had to Well, unless you can provide exact input (commands) and output (error messages) for what you're doing, you're going to stay stuck, unfortunately. install GROMACS 4.0.5 (pre-compiled for Rocks 5.4). This is because We want to know the performance of our cluster. Could you tell me please one BIG...BIG.. inconvenient for this version? I mean, I know that in the web page of GROMACS, one can notice it (http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.0.x), but for me the majority of updates are unknown, as a product of my few experience with the program. Will this version permit us run common calculations (a big range )? Perhaps you can state exactly what you're trying to do. I don't know what a big range of common calculations pertains to. You can run MD with any Gromacs version you like. If you're looking for differences between the 4.0.x series and 4.5.x, you're simply looking in the wrong place. Hundreds of relevant updates are listed here: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x -Justin Thanks in advance. M. --- El *mar, 12/4/11, Justin A. Lemkul /jalem...@vt.edu/* escribió: De: Justin A. Lemkul jalem...@vt.edu Asunto: Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR Para: Miguel Quiliano Meza qil...@yahoo.es Fecha: martes, 12 de abril, 2011 10:20 The complete output from configuration and compilation are unnecessary. The text you posted below is enough to solve this issue. See my post to the list. -Justin Miguel Quiliano Meza wrote: Hi Justin. Sorry if I disturb you for this way. But my message to the GROMACS FORUM has to wait for moderator approval (it`s little big...). For the moment, I consult my doubt for these mail: I wrote... -- Dear community. Justin was right. I did not want to make the explanation so long, but you're right I have to put those details. As you will see I had to redirect the outputs after perform *./configure* and *make* (these files are attach to this mail). I sincerely hope you can give their opinions and help. Thanks in advance. Miguel Quiliano. Here are the general procedure: root@bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz [root@bioinfocluster src]# export LDFLAGS=-L/opt/rocks/lib [root@bioinfocluster src]# export CPPFLAGS=-I/opt/rocks/include [root@bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi --prefix=/share/apps/opt/gromacs output [root@bioinfocluster gromacs-4.5.4]# make output2 mempool.c: In function '_gmx_sel_mempool_alloc_group': mempool.c:201: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c: In function '_gmx_selelem_mempool_reserve': selelem.c:203: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c:208: warning: dereferencing type-punned pointer will break strict-aliasing rules checkpoint.c: In function 'do_cpt_state': checkpoint.c:852: warning: dereferencing type-punned pointer will break strict-aliasing rules /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd_mpi.la http://libmd_mpi.la/] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 -- 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 -- 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
Re: [gmx-users] Differences in default values for nstpcouple and cmap atomtypes between versions 4.0 and 4.5.4
On 13/04/2011 2:10 AM, Anna Duncan wrote:
Hi,
I've started using version 4.5.4 of gromacs, having previously been
using version 4.0 on an older server.
When I run a simulation on v4.0 everything seems to run fine.
However, when I run the same simulation on v4.5.4, mdrun gives me the
error message:
Making 3D domain decomposition 4 x 3 x 2
starting mdrun 'PROTEIN IN BILAYER'
500 steps, 15.0 ps.
step 0
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
.
.
.
.
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
.
.
.
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
Step 25, time 0.75 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.04, max 0.15 (between atoms 147 and 148)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
178179 34.70.2600 0.2600 0.2600
Step 28, time 0.84 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 19.241184, max 126.849724 (between atoms 35 and 36)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 28, time 0.84 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.739422, max 8.610986 (between atoms 496 and 497)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
45 46 90.00.2650 0.5083 0.2650
35 36 90.00.3100 39.6334 0.3100
42 43 90.00.2600 1.2129 0.2600
45 46 90.00.2650 0.5083 0.2650
482483 90.00.2600 0.8649 0.2600
496497 90.00.2700 2.5950 0.2700
496498 90.00.2700 1.4511 0.2700
497498 90.00.2700 2.5822 0.2700
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
This looks like a standard case of
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, which can
be quite situation dependent. In the absence of further information, I'd
guess that 4.0 got lucky with the numerical integration, and 4.5.4 didn't.
I've run g_gmxdump/gmxdump to get the input parameters for the
simulations using the 2 different versions,
gmxcheck is a good tool for comparing various file types.
which I can't attach because they're too big but which differ in the
lines shown below (v4.0 on the left and v4.5.4 on the right):
nstcomm = 1 | nstcomm = 10
nstcalcenergy= 1 | nstcalcenergy= 10
nsttcouple = 1 | nsttcouple = 10
nstpcouple = 1 | nstpcouple = 10
The heuristics by which these are set by default have changed. These
values are not of themselves indicative of a problem.
rgbradii = 2 | rgbradii = 1
sa_surface_tension = 2.092 | sa_surface_tension = 2.05016
sc_sigma_min = 0 | sc_sigma_min = 0.3
nstdhdl = 1 | nstdhdl = 10
These only matter if you're using the relevant algorithms, for which the
defaults have apparently changed.
and also for cmap atomtypes values:
in v4.0:
atomtype[ 0]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 1]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 2]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 3]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 4]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 5]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 6]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 7]={radius= 0.0e+00, volume= 0.0e+00,
gb_radius= 0.0e+00, surftens=-1.0e+00, atomnumber= -1, S_hct=
0.0e+00)}
atomtype[ 8]={radius= 0.0e+00, volume=
Re: [gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 : ERROR
On 13/04/2011 3:38 AM, Miguel Quiliano Meza wrote: Hi everyone. I followed the steps in http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites for my problem, but I obtained problems at the moment to perform make. So, as mention the web page of gromacs... If you get errors during GROMACS compilation (the make step) that suggest that you recompile with -fPIC, then you should return to this FFTW stage and configure with |--enable-shared|or |--with-pic|. By the way, previously I performed make with FFTW version 3.2.2 (default version in rocks cluster 5.4) I did: root@bioinfocluster fftw-3.2.2]# ./configure --enable-threads --prefix=/share/apps/opt/fftw Without errors, and then: [root@bioinfocluster fftw-3.2.2]# make make[3]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' Making all in m4 make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4' make[1]: Leaving directory `/share/apps/src/fftw-3.2.2' What could be the problem? please advices. The problem is probably that you haven't configured FFTW with --enable-shared. Go back to that step, run make distclean and try to configure again. 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
