[gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?
Hi, I tried to calculate the radial distribution functions for a simple system: a 5nm a side cubic box with 10 Ne atoms and 10 Ar atoms, simulated for 100ns in NVT @ 300K. I was expecting to get an RDF with a peak, stabilizing to 1.0 at long distances. This was the case for the Ne-Ar RDF, but not for the Ne-Ne or Ar-Ar RDFs, which stabilize to about 0.9. I believe this is due to a problem in the normalization of the histograms with respect to the number of pairs available: there are N*N pairs for the Ne-Ar, while N*(N-1) for the Ne-Ne and Ar-Ar case. Did somebody else find an issue like this? I think that the issue may become not evident for a relatively large system, as N*N ~ N*(N-1) for large N. I put the relevant files if somebody wishes to reproduce it here: https://gist.github.com/4085292 I'll appreciate input on this and I can also file a bug if deemed necessary. Take care, Pablo -- Dr. Pablo Englebienne Postdoctoral Researcher *TU Delft / 3mE / Process Energy* /Engineering Thermodynamics (ETh) group/ Building 46 Leeghwaterstraat 44, room 030 2628 CA Delft The Netherlands *T* +31 (0)15 27 86662 tel:+31152786662 *E* p.englebie...@tudelft.nl mailto:p.englebie...@tudelft.nl -- 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(r) does not go to 1 at long r -- bug in g_rdf?
On 2012-11-16 09:12, Pablo Englebienne wrote: Hi, I tried to calculate the radial distribution functions for a simple system: a 5nm a side cubic box with 10 Ne atoms and 10 Ar atoms, simulated for 100ns in NVT @ 300K. I was expecting to get an RDF with a peak, stabilizing to 1.0 at long distances. This was the case for the Ne-Ar RDF, but not for the Ne-Ne or Ar-Ar RDFs, which stabilize to about 0.9. I believe this is due to a problem in the normalization of the histograms with respect to the number of pairs available: there are N*N pairs for the Ne-Ar, while N*(N-1) for the Ne-Ne and Ar-Ar case. Did somebody else find an issue like this? I think that the issue may become not evident for a relatively large system, as N*N ~ N*(N-1) for large N. I put the relevant files if somebody wishes to reproduce it here: https://gist.github.com/4085292 I'll appreciate input on this and I can also file a bug if deemed necessary. Take care, Pablo Thanks for reporting. Can you please make a redmine issue of this and assign it to me? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Strange form of RDF curve
On 2012-11-15 18:53, shch406 wrote: Dear Gromacs users, I tried g_rdf function and have obtained a strange result: usually the RDF curve looks like relaxing oscillations around 1.0 constant level, but in my case it appears to be oscillation around exponent going from 0.0 at zero distance to 1.0 at large distances. Is the RDF obtained correct? I used the command as follows: g_rdf -f MT.trr -s MT.tpr -n rs.ndx -o MT.RD.xvg -bin 0.05 -pbc -rdf res_cog where file MT.trr contains ~150 ps of equilibrated trajectory of 582 residue protein in water; The reference group was chosen Water and the 1 group was taken from index file rs.ndx. The latter group contains two tip NHH groups of charged arginine. (This residue was inspected on exposing to solvent and showed one of the largest solvent accessible surface). Thanks in advance, Igor Shchechkin I think you need to switch the arguments, first side chain then water. -- View this message in context: http://gromacs.5086.n6.nabble.com/Strange-form-of-RDF-curve-tp5003001.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g(r) does not go to 1 at long r -- bug in g_rdf?
Thanks David, I filed bug #1036. Regards, Pablo -- View this message in context: http://gromacs.5086.n6.nabble.com/g-r-does-not-go-to-1-at-long-r-bug-in-g-rdf-tp5003015p5003018.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fe(2+) nonbonded parameters
On Thu, Nov 15, 2012 at 5:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/15/12 12:47 PM, Steven Neumann wrote: So what would you do to get those parameters asap? Get what parameters? The ones shown below (except Cu2+) have no citation and no one has vouched for their authenticity. As such, the decision was made to delete them to prevent anyone from blindly using them, hoping that they are right. Given this information, it would be unwise to use them unless, as I said, you know where they came from and believe them to be suitable. -Justin I found the source of the Fe(2+) parameters below from QM/MC simulations: http://www.sciencedirect.com/science/article/pii/S0009261407014388 Please, see table 1. I think it is a reasonable source for the usage Fe(2+) in aqueous solution with protein. Would you comment please? Steven On Thu, Nov 15, 2012 at 5:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/15/12 12:18 PM, Steven Neumann wrote: Dear Gmx Users, Maybe someone before was simulating Fe(2+) in water and protein system using Charmm27 ff. I am looking for nonbonded parametrs. I found in OPLSAA: ; These ion atomtypes are NOT part of OPLS, but since they are ; needed for some proteins or tutorial Argon simulations we have added them. Cu2+ Cu2+ 29 63.54600 2.000 A2.08470e-01 4.76976e+00 Fe2+ Fe2+ 26 55.84700 2.000 A2.59400e-01 5.43920e-02 Zn2+ Zn2+ 30 65.37000 2.000 A1.95200e-01 9.78219e-01 Ar Ar 18 39.94800 0.000 A3.41000e-01 2.74580e-02 But not sure whether I can use them? These are undocumented parameters that are being removed for the next release. Don't use them unless you can find where they came from and you trust that source. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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 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: Umbrella sampling question
Hi, Blindly defining the center of mass for a group of atoms is not possible in a periodic system such as a typical simulation box. You need some clue as to which periodic copy of every atom that is to be chosen. By providing pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the periodic copy closest to the atom given by pull_pbcatom0. If you have large pullgroups this is necessary to define the inter-group distance in a way that makes sense. If you get different results depending on that setting you really need to figure out which atom is a good center for your calculations. The default behavior is to use the atom whose *index* is in the center of the group. If you for example have a dimeric protein this may correspond to the C-terminus of the first chain or the N-terminus of the second one, which in turn often doesn't coincide with the geometrical center of the group. I suggest you try yet another choice of pull_pbcatom0 that is also close to the center to see if that also give rise to a different distance. As mentioned, the choice of pull_pbcatom0 should not matter as long as the choice allows to figure out how to handle the periodicity. Best, Erik 15 nov 2012 kl. 19.56 skrev Gmx QA: Hi Chris Seems my confusion was that I assumed that the distances in the profile.xvg-file should correspond to something I could measure with g_dist. Turns out it does not. Thank you for helping me sorting out this, I got it now :-) About pull_pbcatom0 though. My box is 2*1.08 nm in all directions: $ tail -n 1 conf0.gro 12.45770 12.45770 17.99590 I am still not sure what pull_pbcatom0 does. You said it should not have any effect on my results, but changing it does result in a different initial distance reported by grompp. In my initial attempts at this, I did not specify anything for pull_pbcatom0, but in the grompp output I get this Pull group natoms pbc atom distance at start reference at t=0 0 21939 10970 1 1 0 2.083 2.083 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data Then, following the advice in the thread I referred to earlier, I set pull_pbcatom0 explicitly in the mdp-file to be an atom close to the COM of the Protein. Then I get from grompp Pull group natoms pbc atom distance at start reference at t=0 0 21939 7058 1 1 0 1.808 1.808 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data As you can see, the initial distance is different (2.083 vs 1.808), and 1.808 is the same as the distance reported by g_dist. Do you have any comments here as to why this is? Thanks /PK What you reported is not what you did. It appears that grompp, gtraj, and g_dist report the same value. Please also report the value that you get from your pullx.xvg file that you get from mdrun, which I suspect will also be the same. The difference that you report is actually between the first FRAME of your trajectory from g_dist and the first LINE of the file from the g_wham output. I see no reason to assume that the values in the output of g_wham must be time-ordered. Also, I have never used g_wham myself (I use an external program to do wham) and so I can not say if you are using it correctly. My overall conclusion is that you need to investigate g_wham output not worry about a new run at this stage. Regarding pull_pbcatom0, there is lots of information on the mailing list about this. It is a global atom number that defines the unit cell for selection of which periodic image of each molecule will be used for the pulling. If all of your box dimensions are 2*1.08 nm, then pull_pbcatom0 will not affect your results. Chris. -- 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 Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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
[gmx-users] Bug (?) with FEP while using particle decomposition in charge transformation
Dear all,
I have faced a very strange results while using the FEP together with particle
decomposition in charge transformation. Situation is as follows:
gromacs-4.5.5, single precision, mpi-run on 32 nodes;
only charges are modified in the topology file (VdW and massess remains the
same for A and B state);
particle decomposition (-pd) option is used.
The combination of this conditions lead to a very strange *.xvg file like this
(lambda=0):
@TYPE xy
@ subtitle T = 300 (K), \xl\f{} = 0
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend dH/d\xl\f{} \xl\f{} 0
@ s1 legend \xD\f{}H \xl\f{} 0.1
0. 7.74067 -2.30013
0.0200 8.83184 -2.08346
0.0400 6.61338 -2.43848
0.0600 3.85357 -2.58843
0.0800 9.49265 -2.03448
0.1000 2.4197 -2.7838
0.1200 4.81406 -2.64074
0.1400 3.79622 -2.83082
0.1600 4.9235 -2.53202
0.1800 7.24284 -2.41357
0.2000 3.79017 -2.68861
0.2200 7.84849 -2.26953
0.2400 10.1044 -2.11132
0.2600 1.89623 -3.10296
0.2800 11.6953 -2.08701
0.3000 11.103 -1.96233
0.3200 4.68676 -2.62905
0.3400 9.83457 -2.11386
0.3600 6.12451 -2.27113
0.3800 8.56351 -2.17592
0.4000 11.0368 -1.93516
0.4200 4.80366 -2.49621
0.4400 9.58472 -2.08431
0.4600 5.04113 -2.60035
The usual file (obtained without -pd) looks like this:
@ title dH/d\xl\f{}, \xD\f{}H
@ xaxis label Time (ps)
@ yaxis label (kJ/mol)
@TYPE xy
@ subtitle T = 300 (K), \xl\f{} = 0
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend dH/d\xl\f{} \xl\f{} 0
@ s1 legend \xD\f{}H \xl\f{} 0.1
0. 7.77708 0.777688
0.0200 10.322 1.03217
0.0400 8.82036 0.882043
0.0600 9.46574 0.946536
0.0800 10.2726 1.02731
0.1000 12.0395 1.20386
0.1200 6.85707 0.685689
0.1400 8.99015 0.899035
0.1600 8.68244 0.868208
0.1800 8.98454 0.898397
0.2000 9.21256 0.921202
0.2200 7.16041 0.716125
0.2400 5.1431 0.514307
0.2600 3.34832 0.334797
0.2800 3.14324 0.314328
0.3000 1.83755 0.183755
0.3200 3.91737 0.391783
0.3400 5.79081 0.579126
0.3600 4.92766 0.492766
0.3800 8.06557 0.806605
0.4000 7.00964 0.700994
0.4200 12.1488 1.21481
So the signs of the dH/dlambda are opposite while using particle decomposition.
There is no such problem while running VdW transformation.
Is it a Gromacs bug or I'm doing something wrong?
With best regards,
Alexey Zeifman
--
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Re: [gmx-users] problem in running md simulation
Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] problem in running md simulation
Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing list
Re: [gmx-users] problem in running md simulation
On 11/16/12 10:10 AM, Kavyashree M wrote: Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. One should not make haphazard changes to cutoffs. They are part of the force field. Changing them without basis can invalidate the force field model. -Justin bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior
Re: [gmx-users] GPU warnings
Hi Thomas, The output you get means that you don't have any of the macros we try to use although your man pages seem to be referring to them. Hence, I'm really clueless why is this happening. Could you please file a bug report on redmine.gromacs.org and add both the initial output as well as my patch and the resulting output. Don't forget to specify version of software you were using. Thanks, -- Szilárd On Thu, Nov 15, 2012 at 3:53 PM, Thomas Evangelidis teva...@gmail.comwrote: Hi Szilárd, This is the warning message I get this time: WARNING: Oversubscribing the available -66 logical CPU cores with 1 thread-MPI threads. This will cause considerable performance loss! I have also attached the md.log file. thanks, Thomas On 14 November 2012 19:48, Szilárd Páll szilard.p...@cbr.su.se wrote: Hi Thomas, Could you please try applying the attached patch (git apply hardware_detect.patch in the 4.6 source root) and let me know what the output is? This should show which sysconf macro is used and what its return value is as well as indicate if none of the macros are in fact defined by your headers. Thanks, -- Szilárd On Sat, Nov 10, 2012 at 5:24 PM, Thomas Evangelidis teva...@gmail.comwrote: On 10 November 2012 03:21, Szilárd Páll szilard.p...@cbr.su.se wrote: Hi, You must have an odd sysconf version! Could you please check what is the sysconf system variable's name in the sysconf man page (man sysconf) where it says something like: _SC_NPROCESSORS_ONLN The number of processors currently online. The first line should be one of the following: _SC_NPROCESSORS_ONLN, _SC_NPROC_ONLN, _SC_NPROCESSORS_CONF, _SC_NPROC_CONF, but I guess yours is something different. The following text is taken from man sysconf: These values also exist, but may not be standard. - _SC_PHYS_PAGES The number of pages of physical memory. Note that it is possible for the product of this value and the value of _SC_PAGE_SIZE to overflow. - _SC_AVPHYS_PAGES The number of currently available pages of physical memory. - _SC_NPROCESSORS_CONF The number of processors configured. - _SC_NPROCESSORS_ONLN The number of processors currently online (available). Can you also check what your glibc version is? $ yum list installed | grep glibc glibc.i6862.15-57.fc17 @updates glibc.x86_64 2.15-57.fc17 @updates glibc-common.x86_64 2.15-57.fc17 @updates glibc-devel.i686 2.15-57.fc17 @updates glibc-devel.x86_642.15-57.fc17 @updates glibc-headers.x86_64 2.15-57.fc17 @updates On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis teva...@gmail.comwrote: I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench benchmark with the following command line: mdrun_intel_cuda5 -v -s topol.tpr -testverlet WARNING: Oversubscribing the available 0 logical CPU cores with 1 thread-MPI threads. 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM That is bizzarre. Could you run with -debug 1 and have a look at the mdrun.debug output which should contain a message like: Detected N processors, will use this as the number of supported hardware threads. I'm wondering, is N=0 in your case!? It says Detected 0 processors, will use this as the number of supported hardware threads. (2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4 ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5 on 4 cores (8 threads) without the GPU. Yet, I don't see any performance gain with more that 4 -nt threads. mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day I guess there is not much point in not using all cores, is it? Note that the performance drops after 4 threads because Hyper-Threading with OpenMP doesn't always help. I have also attached my log file (from mdrun_intel_cuda5 -v -s topol.tpr -testverlet) in case you find it helpful. I don't see it attached. I have attached both mdrun_intel_cuda5.debug and md.log files. They will possibly be filtered by the mailing list but will be delivered to your email. thanksm Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com
Re: [gmx-users] GPU warnings
Hi Albert, Apologies for hijacking your thread. Do you happen to have Fedora 17 as well? -- Szilárd On Sun, Nov 4, 2012 at 10:55 AM, Albert mailmd2...@gmail.com wrote: hello: I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x 1344 CUDA cores), and I got the following warnings: thank you very much. ---**messages--**- WARNING: On node 0: oversubscribing the available 0 logical CPU cores per node with 2 MPI processes. This will cause considerable performance loss! 2 GPUs detected on host boreas: #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC: no, stat: compatible 2 GPUs auto-selected to be used for this run: #0, #1 Using CUDA 8x8x8 non-bonded kernels Making 1D domain decomposition 1 x 2 x 1 * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * We have just committed the new CPU detection code in this branch, and will commit new SSE/AVX kernels in a few days. However, this means that currently only the NxN kernels are accelerated! In the mean time, you might want to avoid production runs in 4.6. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Umbrella sampling question
Thanks Erik! /PK 2012/11/16 Erik Marklund er...@xray.bmc.uu.se Hi, Blindly defining the center of mass for a group of atoms is not possible in a periodic system such as a typical simulation box. You need some clue as to which periodic copy of every atom that is to be chosen. By providing pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the periodic copy closest to the atom given by pull_pbcatom0. If you have large pullgroups this is necessary to define the inter-group distance in a way that makes sense. If you get different results depending on that setting you really need to figure out which atom is a good center for your calculations. The default behavior is to use the atom whose *index* is in the center of the group. If you for example have a dimeric protein this may correspond to the C-terminus of the first chain or the N-terminus of the second one, which in turn often doesn't coincide with the geometrical center of the group. I suggest you try yet another choice of pull_pbcatom0 that is also close to the center to see if that also give rise to a different distance. As mentioned, the choice of pull_pbcatom0 should not matter as long as the choice allows to figure out how to handle the periodicity. Best, Erik 15 nov 2012 kl. 19.56 skrev Gmx QA: Hi Chris Seems my confusion was that I assumed that the distances in the profile.xvg-file should correspond to something I could measure with g_dist. Turns out it does not. Thank you for helping me sorting out this, I got it now :-) About pull_pbcatom0 though. My box is 2*1.08 nm in all directions: $ tail -n 1 conf0.gro 12.45770 12.45770 17.99590 I am still not sure what pull_pbcatom0 does. You said it should not have any effect on my results, but changing it does result in a different initial distance reported by grompp. In my initial attempts at this, I did not specify anything for pull_pbcatom0, but in the grompp output I get this Pull group natoms pbc atom distance at start reference at t=0 0 21939 10970 1 1 0 2.083 2.083 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data Then, following the advice in the thread I referred to earlier, I set pull_pbcatom0 explicitly in the mdp-file to be an atom close to the COM of the Protein. Then I get from grompp Pull group natoms pbc atom distance at start reference at t=0 0 21939 7058 1 1 0 1.808 1.808 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data As you can see, the initial distance is different (2.083 vs 1.808), and 1.808 is the same as the distance reported by g_dist. Do you have any comments here as to why this is? Thanks /PK What you reported is not what you did. It appears that grompp, gtraj, and g_dist report the same value. Please also report the value that you get from your pullx.xvg file that you get from mdrun, which I suspect will also be the same. The difference that you report is actually between the first FRAME of your trajectory from g_dist and the first LINE of the file from the g_wham output. I see no reason to assume that the values in the output of g_wham must be time-ordered. Also, I have never used g_wham myself (I use an external program to do wham) and so I can not say if you are using it correctly. My overall conclusion is that you need to investigate g_wham output not worry about a new run at this stage. Regarding pull_pbcatom0, there is lots of information on the mailing list about this. It is a global atom number that defines the unit cell for selection of which periodic image of each molecule will be used for the pulling. If all of your box dimensions are 2*1.08 nm, then pull_pbcatom0 will not affect your results. Chris. -- 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 Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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
Re: [gmx-users] problem in running md simulation
Oh, I am sorry That is right. But its difficult to find The specific cutoff values to be used for different protocols of cutoff, switch and shift.. different values are stated in different papers.. And original force field paper (eg OPLSAA) does not explicitly specify these values. Any references regarding this will be helpful for the users. bye kavya On Fri, Nov 16, 2012 at 8:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/16/12 10:10 AM, Kavyashree M wrote: Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. One should not make haphazard changes to cutoffs. They are part of the force field. Changing them without basis can invalidate the force field model. -Justin bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in ananyachatter...@iiserkol.ac.**inananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not,
[gmx-users] NMA Fatal Error
Hi Gmxers, I am doing a protein NMA with the mdp file like, === define = -DEFLEXIBLE constraints = none integrator = nm ; emtol = 0.1 emstep = 0.1 nsteps = 4000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) ;vdwtype = switch vdwtype = cut-off rlist = 0.0 ; Cut-off for making neighbor list (short range forces) ;coulombtype = PME-switch ; Treatment of long range electrostatic interactions coulombtype = cut-off ;rcoulomb = 1.2 ; Short-range electrostatic cut-off rcoulomb = 0.0 ;rvdw = 1.2 ; Short-range Van der Waals cut-off rvdw = 0.0 pme_order = 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes pbc = no = However, it shows Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported Since I put Constaints none, I really do not get it. Can someone help me? thanks, Yao -- 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] NMA Fatal Error
On 11/16/12 3:43 PM, Yao Yao wrote: Hi Gmxers, I am doing a protein NMA with the mdp file like, === define = -DEFLEXIBLE constraints = none integrator = nm ; emtol = 0.1 emstep = 0.1 nsteps = 4000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) ;vdwtype = switch vdwtype = cut-off rlist = 0.0 ; Cut-off for making neighbor list (short range forces) ;coulombtype= PME-switch; Treatment of long range electrostatic interactions coulombtype = cut-off ;rcoulomb = 1.2 ; Short-range electrostatic cut-off rcoulomb= 0.0 ;rvdw = 1.2 ; Short-range Van der Waals cut-off rvdw= 0.0 pme_order = 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft= yes pbc = no = However, it shows Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported Since I put Constaints none, I really do not get it. Can someone help me? The problem is a typo. You've set -DEFLEXIBLE instead of -DFLEXIBLE so rather than having flexible water as intended, you've got rigid water via the SETTLE algorithm, and constraints are still present. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Force vs distance plot in pulling simulation?
On 11/16/12 10:45 AM, Gmx QA wrote: Hello gmx-users, I've performed a pulling simulation and obtained a force-vs-time plot and a distance-vs-time plot (xvg-files). Is it common to somehow combine these to get a force-vs-distance-plot using a hacked-together script, or how do people that have experience with pulling generally make such a plot? I have read a bunch of papers where such figures are presented, but there does not seem to be any built-in way in gromacs to make them. I could be wrong, of course. The only solution is to write a simple script that parses out the columns you want. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Fe(2+) nonbonded parameters
On 11/16/12 4:01 AM, Steven Neumann wrote: On Thu, Nov 15, 2012 at 5:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/15/12 12:47 PM, Steven Neumann wrote: So what would you do to get those parameters asap? Get what parameters? The ones shown below (except Cu2+) have no citation and no one has vouched for their authenticity. As such, the decision was made to delete them to prevent anyone from blindly using them, hoping that they are right. Given this information, it would be unwise to use them unless, as I said, you know where they came from and believe them to be suitable. -Justin I found the source of the Fe(2+) parameters below from QM/MC simulations: http://www.sciencedirect.com/science/article/pii/S0009261407014388 Thanks for finding this. I will encourage a citation to be added in the OPLS force field about this. Please, see table 1. I think it is a reasonable source for the usage Fe(2+) in aqueous solution with protein. Would you comment please? It's up to you whether you believe the parameters are reliable enough for whatever it is that you're doing. I can't assess that for you. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] partial charges and radius setting
On 11/16/12 3:12 AM, Rajiv Gandhi wrote: Dear Gmx users, I want to know how to set the particular value of effective partial charges CO ligand in topology file ? For non bonded interaction(12-6 Lennard-Jones potential function) how do i set a radius and well depth parameter for CO ? Parameterization methodology depends on the force field you're using. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Dihedral form
And get the use of radians right!
Mark
On Nov 15, 2012 4:01 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
15 nov 2012 kl. 15.41 skrev Laura Leay:
Thanks Eric,
Just to clarify (I hope this notation is in fact clear):
E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi -
n*phi_o)]
^ this whole equation is Dreiding ^this whole
equation is Dreiding converted to the form in Gromacs
This would mean that:
0.5k in Dreiding = k in Gromacs
n in Dreiding = n in Gromacs
n*phi_o +180 in Dreiding (original form) is phi_s in the Gromacs
notation from the original post
I think that's correct.
I hope this makes sense!
Laura
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Erik Marklund [er...@xray.bmc.uu.se]
Sent: 15 November 2012 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Dihedral form
You could shift the reference angle by pi, which changes the sign of the
cosine.
Best,
Erik
15 nov 2012 kl. 14.25 skrev Laura Leay:
All,
I would like to parameterise the Dreiding force field for use with
Gromacs. One thing I am not sure about is how to parameterise the dihedrals
The Dreiding paper has the form;
E= 0.5k { 1 - cos[ n( phi - phi_o)]}
However I cannot find this form in the Gromacs manual. The closest I
can find in the Gromacs manual is:
E = k [ 1 + cos(n*phi - phi_s) ]
Does anyone know of a way to use the Dreiding form in Gromacs, or to
convert to a form that is more suitable for use with Gromacs?
Many thanks,
Laura
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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[gmx-users] NMA proctocol
Hi Gmxers, For Normal Mode Analysis (NMA), even I did run several rounds to aim for machine precision, with smaller emtol stepwise, it still did not converge to 0.001 and the Fmax is about 0.5 or so. It is just lysozyme in 200 water molecules. I wonder if there is a systematic way to guarantee the convergence, or I have to await luck to come. Because I am pretty sure if I continue with NMA, I will get translational and rotational modes in final eigenfrequencies. thanks, Yao On 11/16/12 3:43 PM, Yao Yao wrote: Hi Gmxers, I am doing a protein NMA with the mdp file like, === define = -DEFLEXIBLE constraints = none integrator = nm ; emtol = 0.1 emstep = 0.1 nsteps = 4000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) ;vdwtype = switch vdwtype = cut-off rlist = 0.0 ; Cut-off for making neighbor list (short range forces) ;coulombtype = PME-switch ; Treatment of long range electrostatic interactions coulombtype = cut-off ;rcoulomb = 1.2 ; Short-range electrostatic cut-off rcoulomb = 0.0 ;rvdw = 1.2 ; Short-range Van der Waals cut-off rvdw = 0.0 pme_order = 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes pbc = no = However, it shows Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported Since I put Constaints none, I really do not get it. Can someone help me? The problem is a typo. You've set -DEFLEXIBLE instead of -DFLEXIBLE so rather than having flexible water as intended, you've got rigid water via the SETTLE algorithm, and constraints are still present. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] NMA proctocol
On 11/16/12 6:44 PM, Yao Yao wrote: Hi Gmxers, For Normal Mode Analysis (NMA), even I did run several rounds to aim for machine precision, with smaller emtol stepwise, it still did not converge to 0.001 and the Fmax is about 0.5 or so. It is just lysozyme in 200 water molecules. Are you using double precision? In any case, it may not be possible to reach such a low Fmax. I'm no NMA expert, but generally isn't an Fmax 1 or so considered acceptable? I wonder if there is a systematic way to guarantee the convergence, or I have to await luck to come. Because I am pretty sure if I continue with NMA, I will get translational and rotational modes in final eigenfrequencies. Again, no expert on NMA, but I doubt you ever prevent the emergence of global translation and rotation, but you simply neglect the first 6 eigenvectors (as is stated in g_nmtraj, for instance). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Gromacs 4.6 segmentation fault with mdrun
Hi Raf, which version of Gromacs did you use? If you used branch nbnxn_hybrid_acc please use branch release-4-6 instead and see whether that fixes your issue. If not please open a bug and upload your log file and your tpr. Roland On Thu, Nov 15, 2012 at 5:13 PM, Raf Ponsaerts raf.ponsae...@med.kuleuven.be wrote: Hi Szilárd, I assume I get the same segmentation fault error as Sebastian (don't shoot if not so). I have 2 NVIDA GTX580 cards (and 4x12-core amd64 opteron 6174). in brief : Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffc07f8700 (LWP 32035)] 0x761de301 in nbnxn_make_pairlist.omp_fn.2 () from /usr/local/gromacs/bin/../lib/libmd.so.6 Also -nb cpu with Verlet cutoff-scheme results in this error... gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1 CMake 2.8.7 If I attach the mdrun.debug output file to this mail, the mail to the list gets bounced by the mailserver (because mdrun.debug 50 Kb). Hoping this might help, regards, raf === compiled code : commit 20da7188b18722adcd53088ec30e5f256af62f20 Author: Szilard Pall pszil...@cbr.su.se Date: Tue Oct 2 00:29:33 2012 +0200 === (gdb) exec mdrun (gdb) run -debug 1 -v -s test.tpr Reading file test.tpr, VERSION 4.6-dev-20121002-20da718 (single precision) [New Thread 0x73844700 (LWP 31986)] [Thread 0x73844700 (LWP 31986) exited] [New Thread 0x73844700 (LWP 31987)] [Thread 0x73844700 (LWP 31987) exited] Changing nstlist from 10 to 50, rlist from 2 to 2.156 Starting 2 tMPI threads [New Thread 0x73844700 (LWP 31992)] Using 2 MPI threads Using 24 OpenMP threads per tMPI thread 2 GPUs detected: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible 2 GPUs auto-selected to be used for this run: #0, #1 Back Off! I just backed up ctab14.xvg to ./#ctab14.xvg.1# Initialized GPU ID #1: GeForce GTX 580 [New Thread 0x73043700 (LWP 31993)] Back Off! I just backed up dtab14.xvg to ./#dtab14.xvg.1# Back Off! I just backed up rtab14.xvg to ./#rtab14.xvg.1# [New Thread 0x71b3c700 (LWP 31995)] [New Thread 0x7133b700 (LWP 31996)] [New Thread 0x70b3a700 (LWP 31997)] [New Thread 0x7fffebfff700 (LWP 31998)] [New Thread 0x7fffeb7fe700 (LWP 31999)] [New Thread 0x7fffeaffd700 (LWP 32000)] [New Thread 0x7fffea7fc700 (LWP 32001)] [New Thread 0x7fffe9ffb700 (LWP 32002)] [New Thread 0x7fffe97fa700 (LWP 32003)] [New Thread 0x7fffe8ff9700 (LWP 32004)] [New Thread 0x7fffe87f8700 (LWP 32005)] [New Thread 0x7fffe7ff7700 (LWP 32006)] [New Thread 0x7fffe77f6700 (LWP 32007)] [New Thread 0x7fffe6ff5700 (LWP 32008)] [New Thread 0x7fffe67f4700 (LWP 32009)] [New Thread 0x7fffe5ff3700 (LWP 32010)] [New Thread 0x7fffe57f2700 (LWP 32011)] [New Thread 0x7fffe4ff1700 (LWP 32012)] [New Thread 0x7fffe47f0700 (LWP 32013)] [New Thread 0x7fffe3fef700 (LWP 32014)] [New Thread 0x7fffe37ee700 (LWP 32015)] [New Thread 0x7fffe2fed700 (LWP 32016)] [New Thread 0x7fffe27ec700 (LWP 32017)] Initialized GPU ID #0: GeForce GTX 580 Using CUDA 8x8x8 non-bonded kernels [New Thread 0x7fffe1feb700 (LWP 32018)] [New Thread 0x7fffe0ae4700 (LWP 32019)] [New Thread 0x7fffcbfff700 (LWP 32020)] [New Thread 0x7fffcb7fe700 (LWP 32021)] [New Thread 0x7fffcaffd700 (LWP 32022)] [New Thread 0x7fffca7fc700 (LWP 32023)] [New Thread 0x7fffc9ffb700 (LWP 32024)] [New Thread 0x7fffc97fa700 (LWP 32025)] [New Thread 0x7fffc8ff9700 (LWP 32026)] [New Thread 0x7fffc3fff700 (LWP 32027)] [New Thread 0x7fffc37fe700 (LWP 32028)] [New Thread 0x7fffc2ffd700 (LWP 32029)] [New Thread 0x7fffc27fc700 (LWP 32031)] [New Thread 0x7fffc1ffb700 (LWP 32032)] [New Thread 0x7fffc17fa700 (LWP 32033)] [New Thread 0x7fffc0ff9700 (LWP 32034)] [New Thread 0x7fffc07f8700 (LWP 32035)] [New Thread 0x7fffbfff7700 (LWP 32036)] [New Thread 0x7fffbf7f6700 (LWP 32037)] [New Thread 0x7fffbeff5700 (LWP 32038)] [New Thread 0x7fffbe7f4700 (LWP 32039)] [New Thread 0x7fffbdff3700 (LWP 32040)] [New Thread 0x7fffbd7f2700 (LWP 32042)] [New Thread 0x7fffbcff1700 (LWP 32043)] Making 1D domain decomposition 2 x 1 x 1 * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * We have just committed the new CPU detection code in this branch, and will commit new SSE/AVX kernels in a few days. However, this means that currently only the NxN kernels are accelerated! In the mean time, you might want to avoid production runs in 4.6. Back Off! I just backed up traj.trr to ./#traj.trr.1# Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein in water' 10 steps,200.0 ps. Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffc07f8700 (LWP 32035)] 0x761de301 in nbnxn_make_pairlist.omp_fn.2 () from /usr/local/gromacs/bin/../lib/libmd.so.6 (gdb)
[gmx-users] Re: hydrophobic contacts
Hi all thanks for your valuable suggestions. But still i'm not clear. I have tried using the .tpr file with make_ndx but the index group is displayed is similar to that of the one with .gro file. I have manually identified the residues and when i ran the g_mindist with the ligand 0f 18 atoms against the residues of 174 atoms i'm getting contacts ranging from 87 to 40. please help me with stepwise instruction as I cant follow the thing. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/hydrophobic-contacts-tp4998153p5003043.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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
