Re: [gmx-users] Double or single precision
[EMAIL PROTECTED] wrote: Hi, can anybody explain me the different uses for the single and the double precison packages. Are there situations that explicitly require a double precision package, and situations when i can use a single precision? Double precision energy minimization is normally recommended before doing normal mode analysis. If doing an NVE simulation is important to you, then with otherwise suitable choices of .mdp parameters, double-precision integration might give better energy conservation. Otherwise, you'd probably be wasting processor time. Search the archives, this question has probably been asked before. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham)
Dechang Li wrote: In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. If you've done an equilibration or EM, the structure can have changed during that. I mean the initial structure is the structure I used to generate the .tpr file for mdrun_mpi. What were your command lines, choices for groups and outputs? The most likely simple explanation is that you haven't done what you think you've done :-) My command lines: g_rms -s md.tpr -f md.trr -o rms_protein.xvg -n index.ndx choices for groups: Select group for least squares fit: Protein Select group for RMSD calculation: Protein Have you used gmxcheck to see if the coordinates in md.tpr match the first frame of md.trr? If you're using constraints then these are probably applied before writing the t=0 md.trr frame, check that. You have managed to avoid one common mistake, which would be to use a .gro or .pdb file as input to -s, and not to realise that these are reduced-precision file formats and thus differences from rounding errors are to be expected. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Hi, Sorry for the incomplete details. Here they are now: I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. After that, I did some simple steepest descent minimization, and followed it up by dynamics. Here is the .mdp file for the runs. There is a preceding 25,000-step simulation where the initial velocities are assigned. The mdp file below is what is being used for equilibrium dynamics. thank you for the suggestions. I will also explore the archives ; ; Input file ; ;- ; BASICS ;- title = dummy-file cpp = /usr/bin/cpp integrator = md tinit = 0 init_step = 25000 nsteps = 10 dt = 0.002 ;- ; BOND PARAMETERS ;- constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes lincs_order = 4 lincs_warnangle = 30 ;- ; OUTPUT CONTROL ;- nstxout = 5000 ; positions nstvout = 5000 ; velocity nstlog = 5000 ; energies to log file nstenergy = 5000 ; energy to energy file ;- ; MISCELLANEOUS ;- comm_mode = linear nstlist = 10 ns_type = grid pbc = xyz ; -- ; NONBONDED INTERACTIONS ; -- coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rlist = 1.0 rvdw= 1.0 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ; --- ; NPT ; --- Tcoupl = berendsen tc-grps = LIP Solvent tau_t = 0.1 0.1 ref_t = 313.0313.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ; --- gen_vel = no ; --- On Fri, Apr 4, 2008 at 6:44 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. And as an aside, broken bonds are only a visualization effect; mdrun doesn't write broken molecules. Also, providing your .mdp file would be of use. -Justin The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? You'll have to describe how you minimized and equilibrated your bilayer before we'll have any idea what's going on. Also have a thorough look through the archives; many users have posted about bilayers exploding (including yours truly). -Justin Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
maria goranovic wrote: Hi, Sorry for the incomplete details. Here they are now: I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. This topology change is probably the source of the problem, and would have been a good thing not to describe as a 128-lipid bilayer simulation with standard parameters. After that, I did some simple steepest descent minimization, and followed it up by dynamics. Here is the .mdp file for the runs. There is a preceding 25,000-step simulation where the initial velocities are assigned. The mdp file below is what is being used for equilibrium dynamics. That's all fine. You should have a close look at the structures leading up to the simulation crashes, and pay attention to all of the warning messages from grompp and error messages from mdrun. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Quoting Mahnam [EMAIL PROTECTED]: In God We Trust Hello GMX users I want to equilibrate my protein in a mix solvent, befor this work, I made a cubic box that it contained 215 spc water and 5 proline molecule (without protein) with 20*20*20 angestrom and then I minimized it. when I do position restrain with NPT ensemble and pressure coupling (for 20 ps) for this box, and the box size increase and big holes are created in the box. Also I can do MD at 100 K after this step, but MD at 200 K is imposible and it says : Grid: 25 x 25 x 25 cells WARNING: your box is exploding! (ncells = 15625) You have probably generated some severe atomic overlap. How did you prepare your system? Command line input would be useful here. Did steepest descents converge to an appropriate potential energy? Have a look here for some general advice: http://wiki.gromacs.org/index.php/blowing_up --- Program mdrun, VERSION 3.3.1 Source code file: gmxfio.c, line: 784 Fatal error: Can not read/write topologies to file type mdp What was the exact command line you issued when executing mdrun? -Justin I attached the mdp file for position restrain step to this mail. whould you please guide my for solving this poblem. Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
In God We Trust Hello GMX users I want to equilibrate my protein in a mix solvent, befor this work, I made a cubic box that it contained 215 spc water and 5 proline molecule (without protein) with 20*20*20 angestrom and then I minimized it. when I do position restrain with NPT ensemble and pressure coupling (for 20 ps) for this box, and the box size increase and big holes are created in the box. Also I can do MD at 100 K after this step, but MD at 200 K is imposible and it says : Grid: 25 x 25 x 25 cells WARNING: your box is exploding! (ncells = 15625) --- Program mdrun, VERSION 3.3.1 Source code file: gmxfio.c, line: 784 Fatal error: Can not read/write topologies to file type mdp I attached the mdp file for position restrain step to this mail. whould you please guide my for solving this poblem. Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ prmd-npt.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] set up topology in free energy calculations
QL, 1. Yes. I'd use version a) because of, the less dummies, the better. 2. Yes 3. Of course, charges have to vanish for dummies, too. Keep the bonded terms. If not, your dummies will diffuse away. Yes, your assumption about dummies is right. Actually, I won't use this system for your first perturbation. Take something simpler. Second, as indicated by point 3, you will have to tackle a disappearing netto charge of -1 (depending on the pH of course). This usually is a problem. There were discussions of PME being problematic here. Morphing an ion to counter that charge difference is possible. However, I think this would lead to a very bad equilibrated system and no reasonable results. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ friendli wrote: Dear Gmx users, I am calculating the mutation free energy from amino acid Asp to Asn as a test job for my practice. I have some questions about setting up the topology file. 1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or simply -OH to -NH2. In topology, O - N. What about the hydrogens, do I need one or two dummy(DUM) atoms? a), DUM - H ; H(of OH) - H(of NH2) b), DUM - H(of NH2); DUM - H(of NH2); H(of OH) to DUM a) or b) should I use? 2, I need to provide the coordinates for the dummy atoms in the .gro file(Asp), right? since otherwise the # of atoms in .top and .gro will mismatch. 3, from the tutorial(methane) I read, the masses of the dummy atom keeps like real atom and the C6 and C12 changes to zero in [atomtypes] to vanish the nonbonded interactions. How to deal with the bonds and the charges for dummy atoms? bonded interactions? I think I am a bit confused by the definition of the dummy atom. I understanding is a dummy atom is a atoms with same mass but no interaction with all other atoms. Is that right? thanks for help and suggestions are appreciate. QL ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf
Dear gmx users, I have a basic query. With respect to which structure are the rmsf values calculated per each atom? is it w.r.t average structure of the protein or the reference structure that we provide using -s option? I dont find any explanation of the output generated using g_rmsf. Please make this clear. Thanks!! Swapna On Mon, Apr 7, 2008 at 5:06 AM, Maik Goette [EMAIL PROTECTED] wrote: QL, 1. Yes. I'd use version a) because of, the less dummies, the better. 2. Yes 3. Of course, charges have to vanish for dummies, too. Keep the bonded terms. If not, your dummies will diffuse away. Yes, your assumption about dummies is right. Actually, I won't use this system for your first perturbation. Take something simpler. Second, as indicated by point 3, you will have to tackle a disappearing netto charge of -1 (depending on the pH of course). This usually is a problem. There were discussions of PME being problematic here. Morphing an ion to counter that charge difference is possible. However, I think this would lead to a very bad equilibrated system and no reasonable results. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ friendli wrote: Dear Gmx users, I am calculating the mutation free energy from amino acid Asp to Asn as a test job for my practice. I have some questions about setting up the topology file. 1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or simply -OH to -NH2. In topology, O - N. What about the hydrogens, do I need one or two dummy(DUM) atoms? a), DUM - H ; H(of OH) - H(of NH2) b), DUM - H(of NH2); DUM - H(of NH2); H(of OH) to DUM a) or b) should I use? 2, I need to provide the coordinates for the dummy atoms in the .gro file(Asp), right? since otherwise the # of atoms in .top and .gro will mismatch. 3, from the tutorial(methane) I read, the masses of the dummy atom keeps like real atom and the C6 and C12 changes to zero in [atomtypes] to vanish the nonbonded interactions. How to deal with the bonds and the charges for dummy atoms? bonded interactions? I think I am a bit confused by the definition of the dummy atom. I understanding is a dummy atom is a atoms with same mass but no interaction with all other atoms. Is that right? thanks for help and suggestions are appreciate. QL ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- The logic of life lies exclusively neither in the most incredible detail, nor in the most sweeping synopsis. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf
SWAPNA wrote: Dear gmx users, I have a basic query. With respect to which structure are the rmsf values calculated per each atom? is it w.r.t average structure of the protein or the reference structure that we provide using -s option? I dont find any explanation of the output generated using g_rmsf. Please make this clear. Look at g_rmsf -h because the reference structure is explained there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] infinite molecule problem - Follow up info
Stop COM of the whole system? 2008/4/6 Bo Zhou [EMAIL PROTECTED]: Dear gmx users, My previous question are: I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. I wonder if it is reasonable, if not, is there any solution for it? Any suggestions would be helpful. Thanks. I have tested one system with infinite crystal only, and it turns out be to quite stable (no collective motion has been found), but when I put some water molecules on it, the crystal surface turns out to be what I have said above. Then I stop the COM motion of the crystal, and it seems ok again, just like what I have found in the simulation system with that crystal only (with stopcm too). However, I get a lot of warnings in the log file as follows: Large VCM(group rest): 0.00015, 0.00094, -0.00022, T-cm: inf Large VCM(group rest): -0.00038, 0.00063, -0.00140, T-cm: inf Large VCM(group rest): -0.00029, 0.00050, -0.00206, T-cm: inf Large VCM(group rest): 0.7, 0.00034, -0.00231, T-cm: inf Large VCM(group rest): 0.7, -0.00043, -0.00213, T-cm: inf .. I have not stop the COM motion of the group SOL, and I really do not know how to understand these warnings. I check the system again, everything seems alright except for these awkward warnings. I'm really out of ideas here. If anyone could give me some suggestions I would really appreciate it! Thanks for your time. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g msd freeze
Dear users, I would like to calculate the mean square displacement. Using the g_msd -f traj.xtc -s input.tpr -n index.ndx -o msd.xvg I get Reading file input.tpr, VERSION 3.3.2(single precision) Reading file input.tpr, VERSION 3.3.2(single precision) Group 0( C) has 1 elements There is one group in the index Reading frame 0 time 0.000 The system always freezes here without any warning or error. I have checked my Input files both visually and using gmxcheck, can not find any problem. Thank you very much for your help. I have tried to find the solution in both manuals and archives (thank you very much for them), you are my last resort. Thank you in advance, Katka Hynstova _ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+worldmkt=en-USform=QBRE___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CPMD and gmx
Dear all, We successfully passed all test with CPMD-gmx and now the time to do md production runs, In examples from interface home page timestep is 1fs but in CPMD papers time step is much less, about 0.12 fs. Could you please advise some papers to read? I found only one paper referencing to CPMD-gmx interface publication. Is any common settings for metal cations? The best that I found is links from http://www.cpmd.org/cpmd_publications.html. Thanks for any comment. -- Best regards, Andrey Andrey V. Golovin Ph.D, Assistant professor tel: +7 (495) 939-5305 Bioengineering and Bioinformatics Department Moscow State University fax: +7 (495) 939-3181 119992 Moscow E-mail: [EMAIL PROTECTED] Russia web: http://rnp-group.genebee.msu.su ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CPMD and gmx
Dear Andrey, The maximum time step depends on whether you're doing Born-Oppenheimer or Car-Parrinello MD. In the case of usual BO MD, you normally want a time step of 0.5-1.0 fs, possibly 2 fs, if you use rigid molecules. In the CP case, you have to use a much smaller time step to make sure that the electronic degrees of freedom remain decoupled from the atomic motion (the whole idea of CP approach is to do more time steps, but with only a single iteration for the electronic structure at each step instead of a full SCF minimization). You can find some introductory reading on this, e.g., at the Dominik Marx group website: http://www.theochem.ruhr-uni-bochum.de/home.en.html 2008/4/7, Andrey V Golovin [EMAIL PROTECTED]: Dear all, We successfully passed all test with CPMD-gmx and now the time to do md production runs, In examples from interface home page timestep is 1fs but in CPMD papers time step is much less, about 0.12 fs. Could you please advise some papers to read? I found only one paper referencing to CPMD-gmx interface publication. Is any common settings for metal cations? The best that I found is links from http://www.cpmd.org/cpmd_publications.html. Thanks for any comment. -- Best regards, Andrey Andrey V. Golovin Ph.D, Assistant professor tel: +7 (495) 939-5305 Bioengineering and Bioinformatics Department Moscow State University fax: +7 (495) 939-3181 119992 Moscow E-mail: [EMAIL PROTECTED] Russia web: http://rnp-group.genebee.msu.su ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error gmxtest
Dear David, while ERROR for dec+water complex test is clear, I do not know what to make of this one: FAILED. Check files in acetonitrilRF from /gmxtest/complex/acetonitrilRF/md.log: Initializing LINear Constraint Solver number of constraints is 526 average number of constraints coupled to one constraint is 0.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.004201766767 0.001573 After LINCS 0.01481482 0.00 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.000121796797 0.45 After LINCS 0.01685686 0.00 Started mdrun on node 0 Thu Apr 3 14:52:16 2008 Initial temperature: 326.674 K Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. --- Program mdrun, VERSION 3.3.2 Source code file: network.c, line: 437 Routine should not have been called: gmx_sumi --- Please advise, thank you! Nadia ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: infinite molecule problem - Follow up info
When I stopCM of the whole system, all running is ok, but I found the infinite surface oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. Then I stopCM of the surface only, I get a lot of warnings about the Large VCM(group rest) (group rest = SOL in my system). Thanks for your attention. Stop COM of the whole system? 2008/4/6 Bo Zhou [EMAIL PROTECTED]: Dear gmx users, My previous question are: I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. I wonder if it is reasonable, if not, is there any solution for it? Any suggestions would be helpful. Thanks. I have tested one system with infinite crystal only, and it turns out be to quite stable (no collective motion has been found), but when I put some water molecules on it, the crystal surface turns out to be what I have said above. Then I stop the COM motion of the crystal, and it seems ok again, just like what I have found in the simulation system with that crystal only (with stopcm too). However, I get a lot of warnings in the log file as follows: Large VCM(group rest): 0.00015, 0.00094, -0.00022, T-cm: inf Large VCM(group rest): -0.00038, 0.00063, -0.00140, T-cm: inf Large VCM(group rest): -0.00029, 0.00050, -0.00206, T-cm: inf Large VCM(group rest): 0.7, 0.00034, -0.00231, T-cm: inf Large VCM(group rest): 0.7, -0.00043, -0.00213, T-cm: inf .. I have not stop the COM motion of the group SOL, and I really do not know how to understand these warnings. I check the system again, everything seems alright except for these awkward warnings. I'm really out of ideas here. If anyone could give me some suggestions I would really appreciate it! Thanks for your time. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error gmxtest
Have a look here: http://www.gromacs.org/pipermail/gmx-users/2007-November/030491.html Perhaps try downloading the new version and re-compiling. -Justin Quoting Nadia Gro [EMAIL PROTECTED]: Dear David, while ERROR for dec+water complex test is clear, I do not know what to make of this one: FAILED. Check files in acetonitrilRF from /gmxtest/complex/acetonitrilRF/md.log: Initializing LINear Constraint Solver number of constraints is 526 average number of constraints coupled to one constraint is 0.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.004201766767 0.001573 After LINCS 0.01481482 0.00 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.000121796797 0.45 After LINCS 0.01685686 0.00 Started mdrun on node 0 Thu Apr 3 14:52:16 2008 Initial temperature: 326.674 K Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. --- Program mdrun, VERSION 3.3.2 Source code file: network.c, line: 437 Routine should not have been called: gmx_sumi --- Please advise, thank you! Nadia Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Langevin Dynamic bd-temp parameter
Hi, I tried to run a md calculation with a bd-temp = 300 line in my file, but it gave a warning: Unknown left-hand 'bd-temp' in a parameter file Did I use the right parameter for setting up the temperature in Langevin Dynamics? Thanks for your help in advance. Simon Sham - You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv chaged the chain names of multi-chain complex?
Hi,
Chain name is very important for some application. But, when I use the
following script to get a minimized structure from a multi-chain complex.
But the chain name was changed. I checked the man trjconv , but I did not
find any information on chain name for trjconv.
pdb2gmx -ff ${forcefield} -f starting.pdb -p ${file}.top -i
${file}.posre.itp -o ${file}.gro ${file}.output.pdb2gmx 21
mdrun -nice 0 -v -s ${file}.input.tpr -o ${file}.minim_traj.trr -c
${file}.minimized.gro -e ${file}.minim_ener.edr -g ${file}.emlog.log
${file}.output.mdrun 21
trjconv -sep -f ${file}.minim_traj.trr -s ${file}.input.tpr -o output.pdb
HHH
2
2
HHH
The starting.pdb has four chain: A B D E
The output file output.pdb has a different chain name: A B C D.
Thanks
--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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Re: [gmx-users] trjconv chaged the chain names of multi-chain complex?
Quoting Liu Shiyong [EMAIL PROTECTED]:
Hi,
Chain name is very important for some application. But, when I use the
following script to get a minimized structure from a multi-chain complex.
But the chain name was changed. I checked the man trjconv , but I did not
find any information on chain name for trjconv.
pdb2gmx -ff ${forcefield} -f starting.pdb -p ${file}.top -i
${file}.posre.itp -o ${file}.gro ${file}.output.pdb2gmx 21
Check the pdb2gmx output; I suspect the renaming happened here. If that is the
case, some simple work with a text editor should fix the problem.
-Justin
mdrun -nice 0 -v -s ${file}.input.tpr -o ${file}.minim_traj.trr -c
${file}.minimized.gro -e ${file}.minim_ener.edr -g ${file}.emlog.log
${file}.output.mdrun 21
trjconv -sep -f ${file}.minim_traj.trr -s ${file}.input.tpr -o output.pdb
HHH
2
2
HHH
The starting.pdb has four chain: A B D E
The output file output.pdb has a different chain name: A B C D.
Thanks
--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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Re: [gmx-users] Langevin Dynamic bd-temp parameter
simon sham wrote: Hi, I tried to run a md calculation with a bd-temp = 300 line in my file, but it gave a warning: Unknown left-hand 'bd-temp' in a parameter file Did I use the right parameter for setting up the temperature in Langevin Dynamics? No. Check out the extensive manual section on Run Parameters Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv chaged the chain names of multi-chain complex?
Liu Shiyong wrote:
Hi,
Chain name is very important for some application. But, when I use
the following script to get a minimized structure from a multi-chain
complex.
But the chain name was changed. I checked the man trjconv , but I did
not find any information on chain name for trjconv.
The .gro file format does not permit chain identifiers. So they were
lost when you wrote ${file}.gro, and re-invented for output.pdb. If I
remember correctly they're also not stored in a .tpr file.
pdb2gmx -ff ${forcefield} -f starting.pdb -p ${file}.top -i
${file}.posre.itp -o ${file}.gro ${file}.output.pdb2gmx 21
mdrun -nice 0 -v -s ${file}.input.tpr -o ${file}.minim_traj.trr -c
${file}.minimized.gro -e ${file}.minim_ener.edr -g ${file}.emlog.log
${file}.output.mdrun 21
trjconv -sep -f ${file}.minim_traj.trr -s ${file}.input.tpr -o
output.pdb HHH
2
2
HHH
The starting.pdb has four chain: A B D E
The output file output.pdb has a different chain name: A B C D.
There's no way to fix this one with GROMACS (at least, as far as I
know). However if you edit your starting.pdb file to have the same kind
of format as output.pdb, then you can use the standard unix utility
programs head, tail, grep, cut and paste to solve this problem. Use
head -n x output.pdb head
tail -n y output.pdb tail
to extract the header and footer to separate files, and then grep out
all of the lines that begin with atom records
grep -e '^ATOM' output.pdb outputatom
grep -e '^ATOM' starting.pdb startingatom
Then
cut -c=z startingatom chainidentifiers
cut -c-1-a outputatom left
cut -c=b- outputatom right
paste -d='' left chainidentifiers right middle
cat head middle tail fixed.pdb
and to clean up
rm head tail outputatom startingatom chainidentifiers middle
You will need to identify the correct numbers for x, y, and z, and a=z-1
and b=z+1. See the man pages for each of these commands to learn more.
Mark
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Re: [gmx-users] g msd freeze
Kateřina Hynštová wrote: Dear users, I would like to calculate the mean square displacement. Using the g_msd -f traj.xtc -s input.tpr -n index.ndx -o msd.xvg I get Reading file input.tpr, VERSION 3.3.2(single precision) Reading file input.tpr, VERSION 3.3.2(single precision) Group 0( C) has 1 elements There is one group in the index Reading frame 0 time 0.000 The system always freezes here without any warning or error. I have If your simulation is long and/or computer slow, then it's possible the calculation is still running. If so, you can experiment with the -b, -e, and -dt flags to make the calculation shorter. See g_msd -h. You can also use other analysis tools to check if the problem is localised or not. Otherwise, how big is the system, how long is the trajectory and what system are you running on? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
