Re: [gmx-users] mdp-settings for charmm36 and lipid apl values
they are) For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2. The value for POPE would have been fine I suppose if it hadn't been for the fact that the APL for POPC is smaller. Should it not be larger than POPE? I notice in the Piggott-paper that they in the supplement for some simulations of POPC also get APL's of around 59-60 (without POPE of course), and that the results depend to some extent also on the usage of TIP3P vs TIP3SP water models. I have been using normal TIP3P here. Could anyone comment on (a) my mdp-file settings, and (b) the resulting APL, and tell me if I should be worried about anything? THANKS -- ___ Patrick FUCHS Dynamique des membranes et trafic intracellulaire Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris !!! ATTENTION, nouveau numéro de téléphone !!! Tel : +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] What is the autocorrelation time
Hi Erik, your examples on H-bond acfs are interesting. I'm wondering about the distinct features which are non-exponential in your examples. What do you mean exactly? Could these features be due to rare (H-bonding) events, or in other words to poor sampling? Intuitively, I'd say that the interpretation of the acf (at least for the decay and the decorelation) is always valid unless maybe if you have very poor statistics. Ciao, Patrick Le 20/05/2012 16:12, Erik Marklund a écrit : Dear Chris, As I see it there one can interpret the acf and correlatation time further for certain types of data. I'll use the h-bond autocorrelation function as an example. Here the data is time series of logical true and false, represented as ones and zeros. This type of acf can be direcly interpreted as a probablity, and some quantities derived from the acf can bear further meaning because of this. I also thought that the nature of the data may be such there is a non-exponential part, which makes the autocorreltaion time less valid, or less connected to other intuitive concepts. Again, the h-bond acf has distinct features which are non-exponential and the autocorreltaion time derived from such acfs may in fact be misleading when the h-bond kinetics is to be determined. Hope that makes sense. I's be happy to hear from you if you disagree. Best, Erik 19 maj 2012 kl. 04.01 skrev Christopher Neale: Dear Erik: I thought about your comment for a while and I have come to understand that you are correct. The exponential (or integral) autocorrelation time is a mathematical construct and is defined as such. What I was looking for was an interpretation of the autocorrelation time in terms of the time required to decorrelate the sampling. As to whether or not this will depend on the nature of the data, I don't really understand your conjecture. If the interpretation of the autocorrelation time depends on the nature of the data, then that implies to me that a single scalar value is useless in this case. I don't understand how it could be useful to represent the autocorrelation time by a single number if that number does not mean anything on its own. If you have time, I would appreciate if you could elaborate on this point. Thank you, Chris. -- original message -- Aren't you looking for an interpretation rather than a definition? And will this not depend on the nature of the data? Best, Erik -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] What is the autocorrelation time
Hi Chris, I understand your question, this autocorrelation time puzzled me for a long time as well. Not far from the interpretation you give, Scott Feller defines it (http://dx.doi.org/10.1007/978-1-59745-519-0_7) as the time a given observable takes to lose the memory of its previous state, or in other words the time it takes to relax (that's why it's sometimes called relaxation time). He also discusses it as a tool to choose the block size for calculating an error estimate of an observable (one single simulation can be used as independant samples if each block size is autocorrelation time). We also had a nice discussion some years ago on the mailing list on free energy calculation and error estimate: http://lists.gromacs.org/pipermail/gmx-users/2007-May/027281.html. John Chodera pointed me to a useful article from Wolfhard Janke (the link in the discussion is broken, here's the new one: http://www2.fz-juelich.de/nic-series/volume10/janke2.pdf). There you'll find a rigorous mathematical definition of autocorrelation time. Quoting this paper This shows more clearly that only every 2 tau_int iterations the measurements are approximately uncorrelated and gives a better idea of the relevant effective size of the statistical sample (tau_int is the integrated autocorrelation time; as you said the autocorrelation function is usually a single exponential, but sometimes it's more complex and one needs to evaluate it by integration of the autocorrelation function). After all these considerations, the autocorrelation time can be seen as a tool to assess the time that is needed to have a good estimate of an observable: the simulation must be many many times longer than the autocorrelation time. And sometimes it's directly related to experimental observables (i.e. NMR relaxation experiments). Hope it's useful, Patrick Le 16/05/2012 23:39, Christopher Neale a écrit : Thank you Stephane. Unfortunately, neither of those links contains the information that I am seeking. Those links contain some example plots of autocorrelation functions including a discussion of time-spans over which the example time-series is autocorrelated and when it is not, but neither link defines the (exponential or integral) autocorrelation time except to show a plot and indicate when it is non-zero and when it fluctuates about zero. For example, I already know that the autocorrelation time describes the exponential decay of the correlation and that two values drawn from the same simulation are statistically independent if they are separated by a sufficient number of (accurate) autocorrelation times, but this information is not exactly a definition of the autocorrelation time. I am hoping to find a definition of the autocorrelation time in terms of the probability of drawing uncorrelated samples, although any complete definition will do. If anybody else has the time, I would appreciate it. Thank you, Chris. -- original message -- Probably these links give you simple and clear response for your question http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html and http://www.statsoft.com/textbook/time-series-analysis/ HTH Stephane -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] a question about ensemble
Interesting discussion indeed. I'm just thinking that there might be no fundamental difference to other thermostats. There's nothing in the way that causes the friction, but then again, there's no physical particle that causes the stochastic term in v-rescale, and the Nosé-Hover particle is not physically touching the atoms either. In all cases the surroundings couples to the atoms in a way that can't be seen in e.g. a test tube. Erik Hi Erik, yes, that is a good point, which I haven't really thought about. Indeed, in a macroscopic system heat will have to diffuse from the edges of the container to the inside of the system. In the simulations, the rescaling of velocities is done on all the atoms at the same time, either on a local or global basis. For the use of SD in explicit systems, the friction and stochastic terms (with the carefully chosen friction coeffictient) can be seen as applying one thermostat per degree of freedom. So Florian, I think you should change your view about the random kicks and friction as a way to modify velocities for thermostating, which is different from mimicking solvant effects in implicit simulations (even if it uses also the friction and random forces). What we want is that the thermostat samples the proper canonical ensemble. Then if it does, what also matters is to be aware whether it affects other properties, notably dynamics (because rescaling velocities will in general pertubs dynamics). There has been a nice discussion some years ago in the GROMACS mailing list about that: http://lists.gromacs.org/pipermail/gmx-users/2008-July/035302.html. Also Bussi and Parrinello discuss this aspect in that paper: http://dx.doi.org/10.1016/j.cpc.2008.01.006. Ciao, Patrick -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] a question about ensemble
Hi Florian, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. The use of Langevin dynamics (SD) to mimic solvant implicitely or as a thermostat in explicit systems depends on the friction coefficient you choose. It has to be chosen with care, see for example http://dx.doi.org/10.1007/b99427 or the GROMACS manual. In explicit simulations, SD with the appropriate choice of friction coefficient can be seen as a local thermostat. The advantage is that it samples the canonical ensemble (in the old versions of GROMACS it was the only way to get the canonical ensemble before the implementation of Nose-Hoover or velocity rescaling). Ciao, Patrick -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] REST simulation
Hi Otto, you have to equilibrate at each lambda value! The unscaled Hamiltionian is your lowest temperature, say 300K, which corresponds to lambda=0. You generate the highest temperature by appropriately scaling the Hamiltonian, say 600K, which corresponds to lambda=1. Then you create n directories, one for each replica. In each directory, you set a different lambda value from 0 to 1 in the mdp file and you equilibrate each replica. At the end, you obtain n gro files that can serve as input to generate n tpr files for the REMD run. I think this is the standard flow for REMD as explained in: http://www.gromacs.org/Documentation/How-tos/REMD. The only difference is that you use a different lambda value, so a different Hamiltonian, instead of a different temperature for each replica. Ciao, Patrick Le 13/12/2011 11:46, Otto Master a écrit : Hi Patrick, thanks for your help. What I still do not understand is, how I can set-up the replica simulation starting from the two equilibrated systems. What do I have to put into the .mdp file and in the grompp command to consider the two equilibrated configurations and further obtain the tpr files for the different replica for different lambda values to interpolate between the two configuration. I would be very glad if you could help me on that. All the best Otto On Mon, Dec 12, 2011 at 1:50 PM, Patrick Fuchs patrick.fu...@univ-paris-diderot.fr mailto:patrick.fu...@univ-paris-diderot.fr wrote: Hi Otto, yes I copied those two files you mentionned (also .rtp for charges) in some specific directory to apply the appropriate scaling. But according to the authors this REST implementation, you just need that for the highest temperature (for the lowest, the Hamiltonian is unchanged) and then intermediate temperatures are interpolated using the lambda factor. So for equilibrating each replica, you just need to set the appropriate lambda value. Now I'd consider Mark's advice to use the -pp flag of grompp which might be convenient for scripting the scaling of the potential. Ciao, Patrick Le 12/12/2011 12:56, Otto Master a écrit : Hi Patrick, Thanks a lot for your reply. Just to be sure, you create for every replicate a copy of the original force field, and after you manipulate the parameter in ffnonbonded.itp and ffbonded.itp. Then you go for each replicate through the usual simulation preparation steps (minimisation, nvt, equilibration ...). The result of this you use for the replicate exchange simulation. Thanks a lot Otto On 12 Dec 2011, at 10:42, Patrick Fuchspatrick.fuchs@univ-__paris-diderot.fr mailto:patrick.fu...@univ-paris-diderot.fr wrote: Hi Otto, in my lab we tried to implement this REST variant in GROMACS as proposed by those authors. We figured out that it was easier to manipulate directly the parameters files in the top directory. There you know exactly what you are doing; recall that some interactions (i.e. solvent/solvent) mustn't be scaled whereas some others have to be scaled (solute/solute and solute/solvent). It's probably possible to do it in the tpr file, but it looked less trivial to me: i) you have to know how atoms are coded in the file (e.g. in the functype[???]=LJ_SR[...] matrix, you have to understand how atom numbers are coded there), ii) you have to regenerate a tpr from plain text file; it's probably doable, but I don't know how. Actually, maybe some developers can tell if it's possible. Good luck, Patrick Le 08/12/2011 19:01, Otto Master a écrit : Dear gromacs users, Recently I stumbled over following paper: T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS. Journal of Computational Chemistry 32 (2011) 1228-1234. The authors suggested an easy way to run this kind of simulation with Gromacs, without even changing the code. The only thing that is need, is the the rescaling of the parameters in the parameter file. Since the reduction of the replica number is quite appealing to me I wonder which file I have to change? Actually, I thought of manipulating the .tpr file or to rescale and creating the force fields for every replicate. Is this feasible, or is there a better way? Manipulating the .tpr file could be easier, since
Re: [gmx-users] REST simulation
Hi Otto, do you know how to use the free energy code in GROMACS for running alchemical transformations (such as thermodynamic integration)? I strongly suggest first to be confortable with that code before trying to implement REST. In such alchemical calculations, you have to specify two topologies, one for state A and one for state B. Then simulations at each lambda value is a linear interpolation between state A and state B, such as H = (1-lambda)*H[A] + lambda*H[B]. In the case of REST, one simulation at an intermediate lambda value is also a linear interpolation between topology A (ref T, unscaled Hamiltonian) and topology B (highest T, scaled Hamiltonian). You thus have to build a topology for both A *and* B (how to do that is well described in the manual). Once you have this dual topology, you just have to set lambda for each replica. Ciao, Patrick Le 13/12/2011 14:05, Otto Master a écrit : Hi Patrick, again thanks a lot for your valuable help. But I do not get my head around how to tell grompp that for lambda=0 I would like to use the the unscaled Hamiltonian and for lambda=1 the highest temperature. In the tutorial the change in temperature is a number which is passed to the pre-processor, but for REST a number (lambda=0 and lambda=1) corresponds to different topology, which are written in a file. I do not know how to specify that. What is the identifier or should I pass something additionally to grompp, referring to the two topology files? Ciao, Otto On Tue, Dec 13, 2011 at 1:23 PM, Patrick Fuchs patrick.fu...@univ-paris-diderot.fr mailto:patrick.fu...@univ-paris-diderot.fr wrote: Hi Otto, you have to equilibrate at each lambda value! The unscaled Hamiltionian is your lowest temperature, say 300K, which corresponds to lambda=0. You generate the highest temperature by appropriately scaling the Hamiltonian, say 600K, which corresponds to lambda=1. Then you create n directories, one for each replica. In each directory, you set a different lambda value from 0 to 1 in the mdp file and you equilibrate each replica. At the end, you obtain n gro files that can serve as input to generate n tpr files for the REMD run. I think this is the standard flow for REMD as explained in: http://www.gromacs.org/__Documentation/How-tos/REMD http://www.gromacs.org/Documentation/How-tos/REMD. The only difference is that you use a different lambda value, so a different Hamiltonian, instead of a different temperature for each replica. Ciao, Patrick Le 13/12/2011 11:46, Otto Master a écrit : Hi Patrick, thanks for your help. What I still do not understand is, how I can set-up the replica simulation starting from the two equilibrated systems. What do I have to put into the .mdp file and in the grompp command to consider the two equilibrated configurations and further obtain the tpr files for the different replica for different lambda values to interpolate between the two configuration. I would be very glad if you could help me on that. All the best Otto On Mon, Dec 12, 2011 at 1:50 PM, Patrick Fuchs patrick.fuchs@univ-paris-__diderot.fr mailto:patrick.fu...@univ-paris-diderot.fr mailto:patrick.fuchs@univ-__paris-diderot.fr mailto:patrick.fu...@univ-paris-diderot.fr wrote: Hi Otto, yes I copied those two files you mentionned (also .rtp for charges) in some specific directory to apply the appropriate scaling. But according to the authors this REST implementation, you just need that for the highest temperature (for the lowest, the Hamiltonian is unchanged) and then intermediate temperatures are interpolated using the lambda factor. So for equilibrating each replica, you just need to set the appropriate lambda value. Now I'd consider Mark's advice to use the -pp flag of grompp which might be convenient for scripting the scaling of the potential. Ciao, Patrick Le 12/12/2011 12:56, Otto Master a écrit : Hi Patrick, Thanks a lot for your reply. Just to be sure, you create for every replicate a copy of the original force field, and after you manipulate the parameter in ffnonbonded.itp and ffbonded.itp. Then you go for each replicate through the usual simulation preparation steps (minimisation, nvt, equilibration ...). The result of this you use for the replicate exchange simulation. Thanks a lot Otto On 12 Dec 2011, at 10:42, Patrick Fuchspatrick.fuchs@univ-paris-diderot.fr mailto:patrick.fuchs
Re: [gmx-users] Gromos parameters for atom type OA
Hi, slightly off-thread, I'd like to add that the oxygen parameters of 53a6 have been recently refined in a new set called 53a6OXY (http://pubs.acs.org/doi/abs/10.1021/ct1006407). So this ends up in new values for LJ and charges for the OA atom (as well as for other oxygen atoms). Cheers, Patrick Le 09/12/2011 20:03, Javier Cerezo a écrit : GROMOS force field builds the LJ parameters by multiplication of the square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12) labels). In the case of the repulsion term (C12), up to three of such parameters are possible: SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)), when combined with other atoms, depending on the desired repulsion strength (e.g. the enhanced C12(3) repulsion is used to keep charged groups separated). Which of the three is used depends on the combination of atoms, and is specified in an (asymmetric) matrix (see pages 14 and 15 in the pdf pages of 45a3 and 54a6 force fields from the GROMOS site, or in the ifp file the last lines for each atom type containing 1, 2 and 3). For the case of OA, this matrix specifies that the second C12 term is to be used when OA encountes another OA. So, according, to the ifp line you showed: C12(OA-OA) = SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 * 1.227E-3 = 1.50553E-6 Which is the same for 45a3 and 54a6 force fields. Differences in the parameters will show up only in the cases where the SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2)) Javier El 09/12/11 16:12, Samuli Ollila escribió: Dear all, I was comparing Gromos 45a3 and 53a6 force fields and I found something which I cannot understand. The atom type OA is described in ffG45a3nb.itp as: ;name at.num mass charge ptype c6 c12 OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 and in ffG53a6nb.itp: OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 which are same parameters. However, according to Gromos developers the atom type OA has been changed between Gromos 45a3 and 53a6. The parameters given by Gromos developers for 45a3 are # IAC TYPE SQRT(C6) SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)) 3 OA 0.04756 1.1250E-3 1.227E-3 0.0 and for 53a6 3 OA 0.04756 1.100E-3 1.227E-3 0.0 The actual numbers are different for parameters used in Gromacs since the way to write parameters is different. My problem is that there is difference in OA type between 45a3 and 53a6 in parameters given by Gromos developers but not in the files distributed in Gromacs package. Can someone explain this? BR, Samuli Ollila -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] REST simulation
Hi Otto, in my lab we tried to implement this REST variant in GROMACS as proposed by those authors. We figured out that it was easier to manipulate directly the parameters files in the top directory. There you know exactly what you are doing; recall that some interactions (i.e. solvent/solvent) mustn't be scaled whereas some others have to be scaled (solute/solute and solute/solvent). It's probably possible to do it in the tpr file, but it looked less trivial to me: i) you have to know how atoms are coded in the file (e.g. in the functype[???]=LJ_SR[...] matrix, you have to understand how atom numbers are coded there), ii) you have to regenerate a tpr from plain text file; it's probably doable, but I don't know how. Actually, maybe some developers can tell if it's possible. Good luck, Patrick Le 08/12/2011 19:01, Otto Master a écrit : Dear gromacs users, Recently I stumbled over following paper: T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS. Journal of Computational Chemistry 32 (2011) 1228-1234. The authors suggested an easy way to run this kind of simulation with Gromacs, without even changing the code. The only thing that is need, is the the rescaling of the parameters in the parameter file. Since the reduction of the replica number is quite appealing to me I wonder which file I have to change? Actually, I thought of manipulating the .tpr file or to rescale and creating the force fields for every replicate. Is this feasible, or is there a better way? Manipulating the .tpr file could be easier, since it unifies (right?) the parameters from the different force fields, before sending it to the mdrun application. But for this I would like to understand the tpr file first.There are quite a lot of entries and first I try to understand LJ interactions and how they are defined in this file. I found two entries LJ14 functype[154]=LJ14, c6A= 0.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+00 functype[155]=LJ14, c6A= 4.46680887e-03, c12A= 4.74702711e-06, c6B= 4.46680887e-03, c12B= 4.74702711e-06 which corresponds to following interactions LJ-14: nr: 876 iatoms: 0 type=154 (LJ14) 0 4 1 type=155 (LJ14) 0 5 When I tried to calculate the parameters from the combination rules (in this case Gromos 53A6 force field), I found (the highlighted columns contain the original parameters for the specific atom groups from the Gromos documentation and the calculated value for combining the two parameters: sqrt(C6i) (from ff) sqrt(C6j) (from ff) sqrt(C6i)*sqrt(C6j) value from tpr file functype[154]=LJ14, c6A=CH3 H 0.09805 0 0 0.00E+00 functype[155]=LJ14, c6A=CH3 CH1 0.09805 0.0779 0.007638095 4.47E-03 functype[156]=LJ14, c6A=C CH2 0.04838 0.08642 0.0041813.33E-03 functype[157]=LJ14, c6A=C C 0.04838 0.04838 0.002340624 2.34E-03 The values for N, C, O, H seems to be OK, but I have problems to get the same value, when CH1, CH2, CH3 are involved. Since I do not have too much experience, I would like to know how the value from the .tpr file can be derived. The other entry for LJ potential is the short range term LJ_SR (.tpr file ffparams: atnr=11 ntypes=170 functype[0]=LJ_SR, c6= 9.61380266e-03, c12= 2.66462448e-05 functype[1]=LJ_SR, c6= 4.74365894e-03, c12= 1.14699596e-05 functype[2]=LJ_SR, c6= 4.66325786e-03, c12= 5.1618e-06 Unfortunately, I do not find the section where the function is assigned to a specific pair of interaction. Where are these functions assigned to a specific interaction? Furthermore, is it possible to distinguish between intra-nonbonded (solute-solute) and inter-bonded (water-solute) interaction? For you this might be an easy question to answer, and you immediately realize there is a beginner at work, but nevertheless I would appreciate any help. All the best Otto -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] REST simulation
intra-nonbonded (solute-solute) and inter-bonded (water-solute) interaction? For you this might be an easy question to answer, and you immediately realize there is a beginner at work, but nevertheless I would appreciate any help. All the best Otto -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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 -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] REST simulation
Hi Mark, good to know, this -pp option of grompp is very useful. Thanks! Ciao, Patrick Le 12/12/2011 12:55, Mark Abraham a écrit : On 12/12/2011 8:42 PM, Patrick Fuchs wrote: Hi Otto, in my lab we tried to implement this REST variant in GROMACS as proposed by those authors. We figured out that it was easier to manipulate directly the parameters files in the top directory. There you know exactly what you are doing; recall that some interactions (i.e. solvent/solvent) mustn't be scaled whereas some others have to be scaled (solute/solute and solute/solvent). It's probably possible to do it in the tpr file, but it looked less trivial to me: i) you have to know how atoms are coded in the file (e.g. in the functype[???]=LJ_SR[...] matrix, you have to understand how atom numbers are coded there), ii) you have to regenerate a tpr from plain text file; it's probably doable, but I don't know how. Actually, maybe some developers can tell if it's possible. It's possible, but far from desirable to attempt to manipulate the contents of the .tpr directly. Instead, use grompp -pp to write a complete stand-alone topology, which you can then use as input to a script to do the appropriate solute parameter scaling for each replica. Then use grompp normally on the new set of .top files to generate a set of .tpr files that differ not only in lambda but in their solute parameters. Mark Good luck, Patrick Le 08/12/2011 19:01, Otto Master a écrit : Dear gromacs users, Recently I stumbled over following paper: T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS. Journal of Computational Chemistry 32 (2011) 1228-1234. The authors suggested an easy way to run this kind of simulation with Gromacs, without even changing the code. The only thing that is need, is the the rescaling of the parameters in the parameter file. Since the reduction of the replica number is quite appealing to me I wonder which file I have to change? Actually, I thought of manipulating the .tpr file or to rescale and creating the force fields for every replicate. Is this feasible, or is there a better way? Manipulating the .tpr file could be easier, since it unifies (right?) the parameters from the different force fields, before sending it to the mdrun application. But for this I would like to understand the tpr file first.There are quite a lot of entries and first I try to understand LJ interactions and how they are defined in this file. I found two entries LJ14 functype[154]=LJ14, c6A= 0.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+00 functype[155]=LJ14, c6A= 4.46680887e-03, c12A= 4.74702711e-06, c6B= 4.46680887e-03, c12B= 4.74702711e-06 which corresponds to following interactions LJ-14: nr: 876 iatoms: 0 type=154 (LJ14) 0 4 1 type=155 (LJ14) 0 5 When I tried to calculate the parameters from the combination rules (in this case Gromos 53A6 force field), I found (the highlighted columns contain the original parameters for the specific atom groups from the Gromos documentation and the calculated value for combining the two parameters: sqrt(C6i) (from ff) sqrt(C6j) (from ff) sqrt(C6i)*sqrt(C6j) value from tpr file functype[154]=LJ14, c6A= CH3 H 0.09805 0 0 0.00E+00 functype[155]=LJ14, c6A= CH3 CH1 0.09805 0.0779 0.007638095 4.47E-03 functype[156]=LJ14, c6A= C CH2 0.04838 0.08642 0.004181 3.33E-03 functype[157]=LJ14, c6A= C C 0.04838 0.04838 0.002340624 2.34E-03 The values for N, C, O, H seems to be OK, but I have problems to get the same value, when CH1, CH2, CH3 are involved. Since I do not have too much experience, I would like to know how the value from the .tpr file can be derived. The other entry for LJ potential is the short range term LJ_SR (.tpr file ffparams: atnr=11 ntypes=170 functype[0]=LJ_SR, c6= 9.61380266e-03, c12= 2.66462448e-05 functype[1]=LJ_SR, c6= 4.74365894e-03, c12= 1.14699596e-05 functype[2]=LJ_SR, c6= 4.66325786e-03, c12= 5.1618e-06 Unfortunately, I do not find the section where the function is assigned to a specific pair of interaction. Where are these functions assigned to a specific interaction? Furthermore, is it possible to distinguish between intra-nonbonded (solute-solute) and inter-bonded (water-solute) interaction? For you this might be an easy question to answer, and you immediately realize there is a beginner at work, but nevertheless I would appreciate any help. All the best Otto -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water
Hi Chris, I fully agree with your analysis about the effect of non-bonded interactions that accelerate the collapse when the layer of vacuum around the system is thin. I also observed that it is way faster to reach equilibrium density in this case. Ciao, Patrick Le 23/03/2011 21:06, chris.ne...@utoronto.ca a écrit : Thanks Patrick and Andre! We repeated this with a few box sizes just to get a quick handle on it. The equilibrium volume is about 64 nm^3. If we start with a volume of 1000 nm^3 then the overall box does not collapse at all within 200 ps of NPT Langevin dynamics at 1 atm.If we start with a volume of 200 nm^3, then it does collapse to approximately 64 nm^3 within 200 ps of such simulation. My best guess is that the rapid collapse is driven by nonbonded interactions and thus the rapid collapse does not occur when the system is so large with such low density that water forms isolated vapour droplets that do not interact with each other by LJ interactions. Sure, it is expected to collapse eventually from the 1 atm pressure coupling, and we have also observed that high pressure works, but at 1 atm it might take a very long time to reach equilibrium. I agree with Andre that none of this matters to regular simulations as there is no good reason to go through this type of state when one wants to simulate dense liquids. I just found it curious that Berendsen pressure coupling at 1 atm was not sufficient to quickly equilibrate the volume in a system where the vacuum regions are large in comparison to the LJ cutoffs. Chris. -- original message -- Hi Chris, I experienced the same kind of thing. In the process of building a box of liquid (organic solvent), at some point I wanted to get rid of a layer of vacuum around my system. So for shrinking the box I used similar settings as you and found also that the collapse was going slower than I'd have expected. One solution to accelerate this (if your goal is to shrink the box) is to increase the pressure (to say 100 atm). But it's important to stop the simulation in time (i.e. once the layer of vacuum has disapeared) otherwise the system shrinks too much and density is off. So to come back to your system which has a very big layer of vacuum around, and according to my experience, the volume is probably decreasing but too slowly to see anything signigicant (compared to the initial value) in 200 ps . Ciao, Patrick Le 21/03/2011 16:53, chris.ne...@utoronto.ca a écrit : [Hide Quoted Text] Dear users: I recently came across a system that was composed of tip4p water vapor droplets separated by vacuum. This system is what you might get if you did a NVT simulation of water with a box that was 10 times too large for the number of water molecules. I was surprised to see that this system did not collapse to any significant extent during 200 ps of NPT equilibration at 1 atm using the Berendsen thermostat with tau_p=1.0 and the sd integrator and a colombic cut-off. (We also tried a number of other integrator/pressure coupling combinations with the same results). I had assumed that such collapse would occur quite rapidly. This does not seem to be the case (no noticeable contraction within 200 ps). Has anybody else done anything like this? Can anybody comment on their expectations/experience of collapse from the gas state to the liquid state under standard NPT conditions? Thank you, Chris. -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] compressing a box of water droplets into a homogeneous solution of liquid water
Hi Chris, I experienced the same kind of thing. In the process of building a box of liquid (organic solvent), at some point I wanted to get rid of a layer of vacuum around my system. So for shrinking the box I used similar settings as you and found also that the collapse was going slower than I'd have expected. One solution to accelerate this (if your goal is to shrink the box) is to increase the pressure (to say 100 atm). But it's important to stop the simulation in time (i.e. once the layer of vacuum has disapeared) otherwise the system shrinks too much and density is off. So to come back to your system which has a very big layer of vacuum around, and according to my experience, the volume is probably decreasing but too slowly to see anything signigicant (compared to the initial value) in 200 ps . Ciao, Patrick Le 21/03/2011 16:53, chris.ne...@utoronto.ca a écrit : Dear users: I recently came across a system that was composed of tip4p water vapor droplets separated by vacuum. This system is what you might get if you did a NVT simulation of water with a box that was 10 times too large for the number of water molecules. I was surprised to see that this system did not collapse to any significant extent during 200 ps of NPT equilibration at 1 atm using the Berendsen thermostat with tau_p=1.0 and the sd integrator and a colombic cut-off. (We also tried a number of other integrator/pressure coupling combinations with the same results). I had assumed that such collapse would occur quite rapidly. This does not seem to be the case (no noticeable contraction within 200 ps). Has anybody else done anything like this? Can anybody comment on their expectations/experience of collapse from the gas state to the liquid state under standard NPT conditions? Thank you, Chris. -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] Can g_wham support using different temperature for different windows?
along the reaction coordinates, which is the z-distance between peptide and membrane. This figure (http://www.flickr.com/photos/lijg/5467080971/) shows some of the configurations at certain reaction coordinates. Are you not sampling configurations outside of the membrane (i.e. in water)? I would think that would solve your problem. You don't show any configurations in which the peptide is completely dissociated from the membrane. I don't know your objectives, but I would think that if you could completely extract the peptide from the membrane after passing through it, this would solve your problem. (2) In each window, I used the corresponding configuration that generated by the pulling simulation as initial input and run umbrella sampling. The size of each window is 0.15 nm, but close to the bilayer cneter (e.g., -0.6d0.6), I have increased number of windows so that the width of the window is to be 0.05 or 0.1 nm, I also tried to use different force constant in these windows. From the figure (http://www.flickr.com/photos/lijg/5467080971/) , we can classify the peptide conformation to be either extended (interacting with two bilayers) or compact (interacting with only one bilayer). Ideally, the peptide conformation should be similar for d=x and d=-x. The problem is that the configuration of peptide is not symmetric with respect to the bilayer center. For example, the peptide configuration is compact at d=0.6 and d=0.9, but the peptide is extended at d=-0.6 and d=-0.9. This leads Hysteresis. If I use g_wham to generate PMF, then the PMF is not symmetric with respect to the bilayer center. Using more number of windows and different force constant did not remove the problem. In my opinion, at least in some windows, the peptide should sample both compact and extended structure. But what I found is that the windowed Don't pre-judge the model :) Also, as I said before, there is no reason to suspect that MARTINI will produce any meaningful secondary structure changes. It was not parameterized to do so. umbrella simulation depends on the initial peptide conformation. If the initial peptide conformation is compact, then after 100 ns, it is still compact; if the initial peptide in that window is extended, the final configuration is also extended. I also tried to run longer equilibrium time (e.g., 200 ns), but the problem still exists. Sounds like a limitation of the force field model. My question is how to increase sampling of the peptide conformation? I just think of two choices: (1) use high temperature (e.g., 500K) at those bad windows. As I mentioned, I am wondering if g_wham can unbias the effect of using different temperatures in different windows. (2) use REMD in those bad windows. These need a lot of computational resources. Neither of these will be useful in generating a sensible PMF curve. WHAM needs a single temperature for proper weighting. If you start including different temperatures in different regions of phase space, I would imagine the weighting would be completely incorrect. Note that SMD is not the only option for generating starting configurations. If you think that certain orientations or configurations are correct, you can build them yourself, but keep in mind that you'll have to justify this procedure to a skeptical audience. -Justin Is there any other method to deal with the insufficient sampling? Any suggestions are welcome, thanks for your time reading this email! Cheers, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Tuesday, 22 February 2011 11:13:05 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] InflateGRO and trimer simulation
Hi, the new inflategro with the 'doughnut mode' (http://www.csb.bit.uni-bonn.de/inflategro.html) might do what you want. Ciao, Patrick Justin A. Lemkul a écrit : On 1/10/10 5:17 AM, KM wrote: Hello Gromacs Users, I would like to run a simulation of a trimer in a DPPC membrane. I really like the elegant solution that inflategro script offers, however I'm afraid I won't be able to use it, because I need to have lipids in a small space between the monomers right in the center of the box and these will certainly get deleted during the whole procedure. I also need to keep the waters that come with the structure of the protein. Do you have any idea how I can elegantly embed my trimer in a membrane, possibly using somehow modified inflategro? Christopher I've built multimeric systems with InflateGRO, but with a lot less constraints than you have :) You can, for instance, run an inflation step with a very minimal scaling factor (like 1.01 or 1.05) and a very small cutoff (7 or so, but you'd have to play around with this) so you essentially delete lipids in place without moving them too much. I don't know if the necessary lipids between the monomers will be affected. As for preserving water molecules, you could probably just extract their coordinates from a suitably-oriented starting structure and paste them into the InflateGRO output. None of this requires modifying InflateGRO, but will likely require a lot of trial and error, if it even works, given the very specific nature of what you need. -Justin -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] P-N vector orientation
Hi, as Nicolas suggested you can use my program g_tilt to do such an analysis. Instead of giving the whole backbone as a selection, simply give the 2 atoms (P N). Initially g_tilt uses the first eigen vector of the inertia matrix of the atom selection, so you might want to simplify the code to calculate the PN vector (using [xN-xP,yN-yP,zN-zP]). Ciao, Patrick Nicolas a écrit : Hello, I just remember that you might be interested by g_tilt developed by Patrick Fuchs.: http://www.dsimb.inserm.fr/~fuchs/download/ http://www.dsimb.inserm.fr/%7Efuchs/download/ Its purpose is to calculate the orientation of an helix in a bilayer, however it might tweaked to calculate the NP dipole orientation. I've done that one time, but it was only for a particular lipid in a membrane, not for the whole bilayer. IIRW, the result was the same than the one of my scripts and the calculation was much faster. Nicolas ANINDITA GAYEN a écrit : Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
in lam_ssi_rpi_usysv_proc_read_env () Missing separate debuginfos, use: debuginfo-install e2fsprogs-libs-1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64 libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64 libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64 libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64 (gdb) where #0 0x00770c70 in lam_ssi_rpi_usysv_proc_read_env () #1 0x00784a39 in lam_ssi_rpi_usysv_advance_common () #2 0x0074a1e0 in _mpi_req_advance () #3 0x0073ea90 in MPI_Wait () #4 0x0074d800 in MPI_Sendrecv () #5 0x004aebfd in gmx_sum_qgrid_dd () #6 0x004b40bb in gmx_pme_do () #7 0x00479a58 in do_force_lowlevel () #8 0x004d1d32 in do_force () #9 0x004214d2 in do_md () #10 0x0041bea0 in mdrunner () #11 0x00422b94 in main () (gdb) === Cheers, Patrick Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
...? Cheers, Patrick Berk Hess a écrit : Hi, If your simulations no longer produce output, but still run and there is no error or warning message, my guess would be that they are waiting for MPI communication. But the developers any many users are using 4.0 and I have not heard from problems like this, so I wonder if the problem could be somewhere else. Could you (or have your tried to) continue your simulation from the last checkpoint (mdrun option -cpi) before the hang, to see if it crashes quickly then? Berk Date: Fri, 12 Dec 2008 13:42:43 +0100 From: bernhard.kn...@meduniwien.ac.at To: gmx-users@gromacs.org Subject: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Mark wrote: What's happening in the log files? What's the latest information in the checkpoint files? Could there be some issue with file system availability? Hi Mark Unfortunaltey I already deleted the simulation files which got stuck after 847ps. But here is the output of another simulation done on the same system but with an other pdb file. This one gets stuck after 179ps with the following output: The latest thing the checkpoint file says is: imb F 3% step 89700, will finish Wed Jul 1 09:11:00 2009 imb F 3% step 89800, will finish Wed Jul 1 09:02:51 2009 The predcition for 1st of July is not surprising since I am always parameterizing the simulation with 200ns to avoid to restart it if something interesting happens in the last frames. for the .log file it is: Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.83753e+03 3.64068e+03 2.45951e+03 1.29167e+03 5.13688e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 4.57648e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05 DD step 88999 load imb.: force 3.1% Step Time Lambda 89000 178.2 0.0 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 8.03089e+03 3.59681e+03 2.42628e+03 1.20942e+03 5.12341e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93239e+06 3.09508e+02 1.64627e+01 2.08518e-05 the disk is also free df -h says 2.3G out of 666G used. The only difference between the system with gromacs 3.3 and gromacs 4 is that gromacs 4 is running under suse 11 while gromacs 3.3 is running on a node with suse 10. But I dont think this can be the problem? cheers Bernhard ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
Hi Berk, I tried this fix, but mdrun_mpi is still hanging. I'll try to use the debugger by the end of the week and let you know. Cheers, Patrick Berk Hess a écrit : Hi, My guess is that this is not the problem. But it is very easy to try, so please do. The diff for src/gmxlib/pbc.c is: 392c392,393 try[d] == 0; --- try[d] = 0; pos[d] = 0; Berk Date: Tue, 6 Jan 2009 18:37:20 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi, I also fixed a problem with unitialized variables for pbc calculations in trilinic boxes. But up till now I have not observed any effect of this bug. Is your box triclinic? Yes it is. So shall I test your corrected version ? Patrick Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
it is: Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.83753e+03 3.64068e+03 2.45951e+03 1.29167e+03 5.13688e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 4.57648e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05 DD step 88999 load imb.: force 3.1% Step Time Lambda 89000 178.2 0.0 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 8.03089e+03 3.59681e+03 2.42628e+03 1.20942e+03 5.12341e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93239e+06 3.09508e+02 1.64627e+01 2.08518e-05 the disk is also free df -h says 2.3G out of 666G used. The only difference between the system with gromacs 3.3 and gromacs 4 is that gromacs 4 is running under suse 11 while gromacs 3.3 is running on a node with suse 10. But I dont think this can be the problem? cheers Bernhard ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
I already deleted the simulation files which got stuck after 847ps. But here is the output of another simulation done on the same system but with an other pdb file. This one gets stuck after 179ps with the following output: The latest thing the checkpoint file says is: imb F 3% step 89700, will finish Wed Jul 1 09:11:00 2009 imb F 3% step 89800, will finish Wed Jul 1 09:02:51 2009 The predcition for 1st of July is not surprising since I am always parameterizing the simulation with 200ns to avoid to restart it if something interesting happens in the last frames. for the .log file it is: Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.83753e+03 3.64068e+03 2.45951e+03 1.29167e+03 5.13688e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 4.57648e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05 DD step 88999 load imb.: force 3.1% Step Time Lambda 89000 178.2 0.0 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 8.03089e+03 3.59681e+03 2.42628e+03 1.20942e+03 5.12341e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93239e+06 3.09508e+02 1.64627e+01 2.08518e-05 the disk is also free df -h says 2.3G out of 666G used. The only difference between the system with gromacs 3.3 and gromacs 4 is that gromacs 4 is running under suse 11 while gromacs 3.3 is running on a node with suse 10. But I dont think this can be the problem? cheers Bernhard ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
2.42628e+03 1.20942e+03 5.12341e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93239e+06 3.09508e+02 1.64627e+01 2.08518e-05 the disk is also free df -h says 2.3G out of 666G used. The only difference between the system with gromacs 3.3 and gromacs 4 is that gromacs 4 is running under suse 11 while gromacs 3.3 is running on a node with suse 10. But I dont think this can be the problem? cheers Bernhard ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
Hi, I have exactly the same problem under Fedora 9 on a dual-quadricore (Intel Xeon E5430, 2.66 GHz) computer. Gromacs-4.0.2 is hanging (same for gromacs-4.0.0) after a couple of minutes of simulation. Sometimes, it even hangs very quickly before the simulation reaches the writing of the first checkpoint file (in fact the time length before the hang occurs is chaotic, sometimes a couple of minutes, or a few seconds). The CPUs are still loaded but nothing goes to the output (on any file log, xtc, trr, edr...). All gromacs binaries were standardly compiled with --enable-mpi and the latest lam-7.1.4. As Bernhard and Antoine I don't see anything strange in the log file. I have another computer single quadricore (Intel Xeon E5430, 2.66 GHz) under Fedora 8 and the same system (same mdp, topology etc...) is running fine with gromacs-4.0.2 (compiled with lam-7.1.4 as well). So would it be possible that there's something wrong going on with FC9 and lam-7.1.4...? Cheers, Patrick Berk Hess a écrit : Hi, If your simulations no longer produce output, but still run and there is no error or warning message, my guess would be that they are waiting for MPI communication. But the developers any many users are using 4.0 and I have not heard from problems like this, so I wonder if the problem could be somewhere else. Could you (or have your tried to) continue your simulation from the last checkpoint (mdrun option -cpi) before the hang, to see if it crashes quickly then? Berk Date: Fri, 12 Dec 2008 13:42:43 +0100 From: bernhard.kn...@meduniwien.ac.at To: gmx-users@gromacs.org Subject: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Mark wrote: What's happening in the log files? What's the latest information in the checkpoint files? Could there be some issue with file system availability? Hi Mark Unfortunaltey I already deleted the simulation files which got stuck after 847ps. But here is the output of another simulation done on the same system but with an other pdb file. This one gets stuck after 179ps with the following output: The latest thing the checkpoint file says is: imb F 3% step 89700, will finish Wed Jul 1 09:11:00 2009 imb F 3% step 89800, will finish Wed Jul 1 09:02:51 2009 The predcition for 1st of July is not surprising since I am always parameterizing the simulation with 200ns to avoid to restart it if something interesting happens in the last frames. for the .log file it is: Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.83753e+03 3.64068e+03 2.45951e+03 1.29167e+03 5.13688e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 4.57648e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05 DD step 88999 load imb.: force 3.1% Step Time Lambda 89000 178.2 0.0 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 8.03089e+03 3.59681e+03 2.42628e+03 1.20942e+03 5.12341e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93239e+06 3.09508e+02 1.64627e+01 2.08518e-05 the disk is also free df -h says 2.3G out of 666G used. The only difference between the system with gromacs 3.3 and gromacs 4 is that gromacs 4 is running under suse 11 while gromacs 3.3 is running on a node with suse 10. But I dont think this can be the problem? cheers Bernhard ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] flexible organic solvents
Hi, additionally to the remaks of Andreas there are some parameters in the GROMOS force field G53a5/6 for the solvents you want to simulate (see the original paper). A good read of chapter five of the manual and to all the files in the $GMX/share/top directory should let you build those models. Note there's also a decane.itp there, which uses the Ryckaert-Bellemans potential (as in Berger lipids). One comment on the chair to boat (or more exactly twist-boat) transition, the enthalpy barrier has been estimated to ~ 10 kcal/mol by ab initio and MM2 calculations. It is thus unlikely to observe any transition within a few nanoseconds if you start from a chair conformation at room temperature. Ciao, Patrick Kukol, Andreas a écrit : Yes that should be possible without big problems. The Gromacs manual and Wiki pages about how to build a topology is a good starting point. Then you could try the gromacs program x2top to generate a topology, or the Prodrg2 server. Andreas -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sascha Rehm Sent: 14 August 2008 12:03 To: gmx-users@gromacs.org Subject: [gmx-users] flexible organic solvents Dear Gromacs users, I simulate proteins with different organic solvents like toluene, cyclohexane or isopentane. Right now, I used rigid body models for these solvents, made and simulated with Amber. For my future work, I unse Gromacs and need to rebuild these solvents. Can I build a cyclohexane model, which is more flexible and can change from chair conformation to boat conformation and vice versa? And how do I build a non-rigid Isopentane with internal degrees of freedom? Hope, this is not a stupid questions, but I searched quite a while the mailing list and also google, but did nearly find nothing about other common (flexible) solvents. Can someone give me a hint, which keywords I should use to search or where I can find some informations/tutorials/explanations? Thanks a lot, Sascha ___ 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 -- _ new E-mail address: [EMAIL PROTECTED] new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ 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] Problem with lipid simulations
Hi Chandu, this looks like you have two statements #include lipid.itp, so check all your *.top and *.itp files. Ciao, Patrick [EMAIL PROTECTED] a écrit : Dear All, I have been trying to simulate a small peptide in a DMPC lipid bylayer. Same setup is working fine in one computer (cluster) but I am getting the following error message in another cluster. grompp_mpi -f test.mdp -c lipid_protein.gro -p topology.top -o test.tpr checking input for internal consistency... calling /lib/cpp... processing topology... WARNING 1 [file lipid.itp, line 14]: Overriding atomtype LO WARNING 2 [file lipid.itp, line 15]: Overriding atomtype LOM WARNING 3 [file lipid.itp, line 16]: Overriding atomtype LNL WARNING 4 [file lipid.itp, line 17]: Overriding atomtype LC WARNING 5 [file lipid.itp, line 18]: Overriding atomtype LH1 WARNING 6 [file lipid.itp, line 19]: Overriding atomtype LH2 WARNING 7 [file lipid.itp, line 20]: Overriding atomtype LP WARNING 8 [file lipid.itp, line 21]: Overriding atomtype LOS WARNING 9 [file lipid.itp, line 22]: Overriding atomtype LP2 WARNING 10 [file lipid.itp, line 23]: Overriding atomtype LP3 Cleaning up temporary file grompp16bicP --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp_mpi terminated --- Please let me know how to get rid of this problem. Thanks in advance Regards Chandu ___ 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 -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ 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] Gromacs force field discussion
Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, Patrick David van der Spoel a écrit : Reay, Andrew wrote: Hi, I am trying to find out why the Gromacs force field is no longer recommended for use. I've searched the mailing list archives for quite awhile to find the discussion but have been unsuccessful. Can anybody tell me where to find that discussion? Thanks very much. The never has bee a GROMACS force field, although we named it such to avoid confusion with official GROMOS force fields. What used to be called the GROMACS force field was basically GROMOS87 + changes due to Van Buuren Berendsen (J.Phys.Chem. 97 [1993] 9206) plus changes on aromatic groups from an unpublished paper from the Van Gusteren group (these parameters are given in my paper in J.Biomol. NMR 8 (1996) p.229). This is described in the manual. In other words there is no good description of ths force field in a single paper. For good reasons the Van Gunsteren group have updated their GROMOS force field on a number of occasions, and these force field are now supported in GROMACS, along with a few others. Although it is still possible to use the old parameter set, please do not call it The GROMACS force field, but use the description above. Most referees fro scientific papers will (should) raise their eyebrows when reading that this parameter set was used, so this is another reason to shy away from it. Andy ___ 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 -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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_dist producing inconsistent values
Hi, another quick and dirty tip (but at least it works !) is to generate a new trajectory using trjconv with a huge layer of vacuum on the Z direction (assuming your membrane normal is oriented along Z): you can do that with the -box option with a large value for Z. If you just put only the phosphorous atoms in there this won't generate a large file. Cheers, Patrick Alan Dodd a écrit : - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, February 7, 2008 6:35:55 PM Subject: Re: [gmx-users] g_dist producing inconsistent values [EMAIL PROTECTED] wrote: I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math. Distance larger than half a box size are ill-defined anyway in a PBC simulation. -What do you mean? I'd assumed that simply having enough water separating a bilayer from its periodic image that no water 'saw' both bilayers would be sufficient; is this not the case? In some special cases you can do this, for instance within a protein it would work. I've implemented -nopbc options in some programs but not in g_dist yet. Please put it on the developer wishlist. on the wiki. -Done. Until then, I'm using g_traj -ox -com and doing the math with my own script. Many thanks for the various alternative techniques suggested. Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] About g_msd
/users.php 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] About g_msd (and noise)
it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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: Where is the GROMOS87 force field when using pdb2gmx
Hi Erik, but I did read many works in the literature that used G43a*, even yours in BJ (2006). I basically agree that the 'philosophy' of the Berger lipids is derived from OPLS, thus using this latter force field is probably best suited for peptide/lipid simulation in conjunction with Berger lipids (like in Tieleman et al 2006 J. Phys.: Condens. Matter 18 S1221-S1234, or your last paper in press in Proteins). But apart from self-consistency, is it so a problem to mix Berger lipids with a GROMOS derived force field ? I ask you that because *many* previous works used Berger lipids with ffgmx (and this latter is probably still in use even if deprecated). So what is right ? It would probably be worth doing a systematic comparison of the use of different protein force fields with Berger lipids. The above ref of P. Tieleman goes in this direction. Cheers, Patrick Erik Lindahl a écrit : Hi, On Nov 7, 2007, at 5:40 PM, maria goranovic wrote: Thanks for the help, David. Actually, I just realized I was trying to decide based on mailing list archives which, in some cases, are 5 years old. My mistake. I will use the 43a2 field for my protein. Is there any standard procedure to combine 43a2 with the berger force field (ffgmx) for lipids ? Don't do it. The berger force field is mostly derived from OPLS, so you will (again) find it much easier to defend your choices if you mix it with OPLS-AA/L instead. Cheers, Erik ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] what is the force function for proper dihedrals
Hi Chris, I've been searching for this as well. You might get some clues in the following article, but I didn't have time to read it: T. Schlick, A Recipe for Evaluating and Differentiating Cos phi Expressions, J. Comp. Chem., 10:951-956, May (1989) I'm interested if you find any pointer to a book or paper on this issue. Cheers, Patrick Chris Neale a écrit : Hello, The manual does a good job at explaining the potential energy function for all types of interactions. For bonded interactions the manual also describes the force function for every type except dihedrals. The Allan and Tildesley bool also lacks this information. It's one thing to know that the force is the negative gradient of the potential energy, but for proper dihedrals it is not trivial to determine this. If anybody knows the force function for proper dihedrals then I would greatly appreciate a reply. Thanks, Chris. ___ 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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_bundle!
Hi, I wrote a program to calculate the tilt angle between a helix axis and the bilayer normal called g_tilt. It's available here http://condor.ebgm.jussieu.fr/~fuchs/download/. There you'll find also a program to calculate the azimuthal rotation (g_rotation). I plan to upload these contributions on the GROMACS website when I have time :-) Ciao, Patrick priyanka srivastava a écrit : Dear All, I want to calculate tilt angle of a peptide inserted inside the lipid bilayer (i.e. angle between the helical axis and bilayer normal). From previous posts I got an idea that g_bundle wud solve my problem. I am issuing the following on the command line: g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps This asks me to Select a group of top and a group of bottom atoms Group 0 ( System) has 12877 elements Group 1 ( Protein) has 102 elements Group 2 ( Protein-H) has79 elements Group 3 ( C-alpha) has10 elements Group 4 (Backbone) has31 elements Group 5 ( MainChain) has41 elements Group 6 (MainChain+Cb) has49 elements Group 7 ( MainChain+H) has54 elements Group 8 ( SideChain) has48 elements Group 9 ( SideChain-H) has38 elements Group10 ( Prot-Masses) has 102 elements when I chose 1 and 1 it gives all angles as 90, which is wrong and bun_tiltr is reported as nan. The manual says that the program reads two index groups and divides both of them in -na parts. I am a lil confused! what should be my choice here? regards, Pri... Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC ___ 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] Polarizability
Hi, there's a very recent paper of the GROMOS team, where they evaluate the free energy of polarization (with the 'Charge-on-Spring' model): http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html Their code is already working, but under the GROMOS software... Ciao, Patrick Jones de Andrade a écrit : Hi David They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I've found two papers for charmm polariability. But I'll only be able to try to find it in the library or to ask for the authors tomorrow at least. But thanks for the information! ;) On the other hand, I could not yet find any published material from amber using shell models. Is this only an inside group discussion? I think there is not a lot of difference, but shell models are easier to implement. I think too. In reality, there is no visible rational reason for this fear of me, is more like a feeling, so I'll try to find something more on it. But I do agree that it's much likely that the shell model is much easier to implement, if not faster to execute also. :) I am working on shell models a bit (not enough...) Me too. Specially cause this is long terms plans (2+ years from now). But thanks a lot for all information, David. Helped a lot. Sincerally yours, Jones ___ 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] Polarizability
Hi Jones, Charge-on-spring model is another name for shell model. Here's what's written in the introduction of the paper: [...]in the charge-on-spring (or Drude-oscillator or shell) model, an additional point charge is attached to a polarizable center that can adapt its position to the electric field to induce a net dipole.[...] Ciao, Patrick Jones de Andrade a écrit : Hi Patrick. Just got this paper here, thanks for the indication. This may sound like a dumb question, but: am I wrong, or the shell model and the charge on a spring model differ only by the fact that the VdW interation is also floating aroung in the shell model but not in the charge on a spring one? Thanks a lot, Jones On 5/21/07, *Patrick Fuchs* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi, there's a very recent paper of the GROMOS team, where they evaluate the free energy of polarization (with the 'Charge-on-Spring' model): http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html Their code is already working, but under the GROMOS software... Ciao, Patrick Jones de Andrade a écrit : Hi David They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I've found two papers for charmm polariability. But I'll only be able to try to find it in the library or to ask for the authors tomorrow at least. But thanks for the information! ;) On the other hand, I could not yet find any published material from amber using shell models. Is this only an inside group discussion? I think there is not a lot of difference, but shell models are easier to implement. I think too. In reality, there is no visible rational reason for this fear of me, is more like a feeling, so I'll try to find something more on it. But I do agree that it's much likely that the shell model is much easier to implement, if not faster to execute also. :) I am working on shell models a bit (not enough...) Me too. Specially cause this is long terms plans (2+ years from now). But thanks a lot for all information, David. Helped a lot. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] mailto:[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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs
Re: [gmx-users] Very large fluctuations in dg/dl
Hi John, thanks a lot for your reply. Indeed, the standard deviation I presented in my previous post is the one of dg/dl samples. I was just surprised by the fact the std. dev. is always larger than the value itself (since I'm starting with FE calculation I had no expectation of what the behavior would be and needed a confirmation). I was also suprised about the convergence of the mean. I put a plot for each lambda value at the URL: http://condor.ebgm.jussieu.fr/~fuchs/download/convergence.png (at each time step, I recalculate the mean from the beginning). My first observation was that 1 ns seemed to be a minimum for certain lambda values (e.g. lambda=0.70). I sometimes read in literature that some authors used a few hundreds of ps, which seemed (to me) not sufficient for proper convergence. Now, if we come back to the error estimate of the mean, I found (for lambda=0.00) 0.2 kJ/mol using block averaging (using the -ee option of g_analyze), which is reasonable I imagine (even if higher precisions have been described in literature). I'm not sure whether this is the same way of calculating the uncertainty compared to what you proposed. Can you confirm? I will have a look to the book you mentioned, thanks for the pointer. Cheers, Patrick On Mon, 7 May 2007, John D. Chodera wrote: Hi Patrick, I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane (compared to 8.7 in Geerke van Gunsteren, ChemPhysChem 2006, 7, 671 ? 678) but I get really huge fluctuations in the values of dg/dl: lambda=0.00: 5.0 +/- 10.8 (mean +/- standard deviation) lambda=0.05: 4.3 +/- 11.2 Is the standard deviation you quote here the standard deviation of the dg/dl samples, or the standard deviation of the mean? If the former, then this behavior is totally expected: While the standard deviation of a random variable (your dg/dl samples) may be large, with enough sampling, we can get a very precise estimate of the mean. More sampling will not change the standard deviation of the dg/dl samples, but it will reduce the standard error in the mean, which is what we need for precise estimates of free energy differences. The uncertainty in the estimate of dg/dl is given simply by ddg/dl = sigma / sqrt(N / g) where here, sigma is the standard deviation of your dg/dl samples, N is the number of data points you have collected, and g is something called the statistical inefficiency, which can be estimated from the correlation time of your dg/dl samples. More information on this sort of analysis can be found in reference [1] below. Once you have the uncertainty in each estimate of dg/dl, you still have to combine these to get the uncertainty estimate for the integrated free energy difference using standard propagation of error. This depends on your choice of quadrature for TI. David Mobley has done a lot of this, and I'm sure would be willing to help if you had trouble figuring it out. Good luck! - John [1] W. Janke. Statistical analysis of simulations: Data correlations and error estimation. In J. Grotendorst, D. Marx, and A. Murmatsu, editors, Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, volume 10, pages 423?445. John von Neumann Institute for Computing, 2002. -- John Chodera [EMAIL PROTECTED] | Mobile: 415 867-7384 Postdoctoral researcher, Pande lab| Lab phone : 650.723.1097 Department of Chemistry, Stanford University | Lab fax : 650.724.4021 http://www.dillgroup.ucsf.edu/~jchodera -- Date: Mon, 07 May 2007 16:41:26 +0200 From: Patrick Fuchs [EMAIL PROTECTED] Subject: [gmx-users] Very large fluctuations in dg/dl To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=windows-1252; format=flowed Hi Gromacs users, I have a few questions related to solvation free energy calculation via thermodynamic integration. I'm trying to reproduce some literature data (on e.g. methane, methanol...) using the GROMOS G53a6 force field. I followed the tutorial of David Mobley (thanks to him BTW), but I used the standard non bonded options of the G53a6 force field (instead of OPLS). For each lambda value I do a minimization, a 10 ps NVT followed by a 20 ps NPT equilibration, and a 1 ns NVT production using the sd integrator. I used 21 lambda values (0.00, 0.05...1.00). Here's my topology file: begining of methane.top ; topology for a methane molecule ; include GROMOS53a6 force field #include ffG53a6.itp ;;; begin methane definition ;;; [ moleculetype ] ; Name nrexcl METH 3 [ atoms ] ;nr type resnr residue atom cgnr charge masstypeB chargeB massB 1 CH4 1 METHC1 00. 16.0430 DUM 0. 16.04300 ;; end methane definition ; include water topology #ifdef FLEX_SPC #include flexspc.itp #else #include spc.itp #endif [ system ] ; name 1 methane molecule in water [ molecules ] ; name number METH1 SOL
Re: [gmx-users] Very large fluctuations in dg/dl
Hi Berk and Tsjerk, sounds reassuring since the last version of the GROMOS force field (G53a5 and a6) has been parametrized to reproduce DGsol using reaction field. But, you agree Berk that when you want to calculate the solvation free energy in the GROMOS philosophy (e.g. for reproducing or computing new parameters), you have to use RF even if energy conservation might not be as good as with PME? Thanks for your answers and your interest in the thread. Cheers, Patrick On Tue, 8 May 2007, Berk Hess wrote: From: Tsjerk Wassenaar [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Very large fluctuations in dg/dl Date: Tue, 8 May 2007 06:39:50 +0200 Hi Berk, Just a question relating to your reply (should be a new thread maybe...). The Gromos force fields were parameterized (for use) with cutoff/RF. PME is of course better for energy conservation, but the inclusion of the interactions beyond the cut-off may give rise to deviant behaviour from the force field. Could you enlighten me on this issue? Thanks, Tsjerk Luckily it does not. And PME is not only better for energy conservation, but also captures long-range interaction, which for instance leads to more stable proteins. I have compared solvation free energies for G53A6 with reaction-field and PME and found no differences: B. Hess and N. van der Vegt Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 110, 17616 (2006) http://dx.doi.org/10.1021/jp0641029 Berk. On 5/7/07, Berk Hess [EMAIL PROTECTED] wrote: From: Patrick Fuchs [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] Very large fluctuations in dg/dl Date: Mon, 07 May 2007 16:41:26 +0200 Hi Gromacs users, I have a few questions related to solvation free energy calculation via thermodynamic integration. I'm trying to reproduce some literature data (on e.g. methane, methanol...) using the GROMOS G53a6 force field. I followed the tutorial of David Mobley (thanks to him BTW), but I used the standard non bonded options of the G53a6 force field (instead of OPLS). For each lambda value I do a minimization, a 10 ps NVT followed by a 20 ps NPT equilibration, and a 1 ns NVT production using the sd integrator. I used 21 lambda values (0.00, 0.05...1.00). Here's my topology file: begining of methane.top ; topology for a methane molecule ; include GROMOS53a6 force field #include ffG53a6.itp ;;; begin methane definition ;;; [ moleculetype ] ; Name nrexcl METH 3 [ atoms ] ;nr type resnr residue atom cgnr charge masstypeB chargeB massB 1 CH4 1 METHC1 00. 16.0430 DUM 0. 16.04300 ;; end methane definition ; include water topology #ifdef FLEX_SPC #include flexspc.itp #else #include spc.itp #endif [ system ] ; name 1 methane molecule in water [ molecules ] ; name number METH1 SOL 893 -end of methane.top And here is my mdp file for lambda=0: ---begining of prod.mdp- title = production NVT methane/water cpp = /lib/cpp ; OPTIONS FOR BOND CONSTRAINTS constraints = all-bonds ; RUN CONTROL PARAMETERS integrator = sd tinit = 0 dt = 0.002 nsteps = 50 ; 1000 ps ; NUMBER OF STEPS FOR CENTER OF MASS MOTION REMOVAL nstcomm = 100 ; OUTPUT CONTROL OPTIONS nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 100 nstxtcout= 5000 xtc-precision= 1000 ; NON BONDED STUFF ns_type = grid nstlist= 5 rlist = 0.8 coulombtype= generalized-reaction-field rcoulomb = 1.4 rvdw = 1.4 epsilon_rf = 54.0 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ; inverse langevin friction cst ref_t= 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = no tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; FREE ENERGY CONTROL STUFF free_energy = yes init_lambda = 0.00 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 ; VELOCITY GENERATION gen_vel = yes gen_temp = 300 gen_seed = -1 -end of prod.mdp I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane (compared to 8.7 in Geerke van Gunsteren, ChemPhysChem
Re: [gmx-users] Very large fluctuations in dg/dl
Hi Berk, I just wanted a confirmation because it's a critical aspect. Beyond the debate between PME and RF, I always read it was important to be consistent with the (early) force field parameterization when deriving new parameters. Even if it does not make any difference for solvation free energy, I imagine this can give some differences on other properties (e.g. heat of vaporization...), or if you want your new parameters to be consistent with the remaining of the force field. Ciao, Patrick On Tue, 8 May 2007, Berk Hess wrote: Hi, I don't understand why you ask this. Or didn't you read or understand my previous answer? Reaction-field and PME give exactly the same solvation free-energies, so you can just as well derive parameters for the GROMOS force-field using PME. Berk. From: Patrick Fuchs [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Very large fluctuations in dg/dl Date: Tue, 8 May 2007 12:45:32 +0200 (CEST) Hi Berk and Tsjerk, sounds reassuring since the last version of the GROMOS force field (G53a5 and a6) has been parametrized to reproduce DGsol using reaction field. But, you agree Berk that when you want to calculate the solvation free energy in the GROMOS philosophy (e.g. for reproducing or computing new parameters), you have to use RF even if energy conservation might not be as good as with PME? Thanks for your answers and your interest in the thread. Cheers, Patrick On Tue, 8 May 2007, Berk Hess wrote: From: Tsjerk Wassenaar [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Very large fluctuations in dg/dl Date: Tue, 8 May 2007 06:39:50 +0200 Hi Berk, Just a question relating to your reply (should be a new thread maybe...). The Gromos force fields were parameterized (for use) with cutoff/RF. PME is of course better for energy conservation, but the inclusion of the interactions beyond the cut-off may give rise to deviant behaviour from the force field. Could you enlighten me on this issue? Thanks, Tsjerk Luckily it does not. And PME is not only better for energy conservation, but also captures long-range interaction, which for instance leads to more stable proteins. I have compared solvation free energies for G53A6 with reaction-field and PME and found no differences: B. Hess and N. van der Vegt Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 110, 17616 (2006) http://dx.doi.org/10.1021/jp0641029 Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ 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] Very large fluctuations in dg/dl
Hi Gromacs users, I have a few questions related to solvation free energy calculation via thermodynamic integration. I'm trying to reproduce some literature data (on e.g. methane, methanol...) using the GROMOS G53a6 force field. I followed the tutorial of David Mobley (thanks to him BTW), but I used the standard non bonded options of the G53a6 force field (instead of OPLS). For each lambda value I do a minimization, a 10 ps NVT followed by a 20 ps NPT equilibration, and a 1 ns NVT production using the sd integrator. I used 21 lambda values (0.00, 0.05...1.00). Here's my topology file: begining of methane.top ; topology for a methane molecule ; include GROMOS53a6 force field #include ffG53a6.itp ;;; begin methane definition ;;; [ moleculetype ] ; Name nrexcl METH 3 [ atoms ] ;nr type resnr residue atom cgnr charge masstypeB chargeB massB 1 CH4 1 METHC1 00. 16.0430 DUM 0. 16.04300 ;; end methane definition ; include water topology #ifdef FLEX_SPC #include flexspc.itp #else #include spc.itp #endif [ system ] ; name 1 methane molecule in water [ molecules ] ; name number METH1 SOL 893 -end of methane.top And here is my mdp file for lambda=0: ---begining of prod.mdp- title = production NVT methane/water cpp = /lib/cpp ; OPTIONS FOR BOND CONSTRAINTS constraints = all-bonds ; RUN CONTROL PARAMETERS integrator = sd tinit = 0 dt = 0.002 nsteps = 50 ; 1000 ps ; NUMBER OF STEPS FOR CENTER OF MASS MOTION REMOVAL nstcomm = 100 ; OUTPUT CONTROL OPTIONS nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 100 nstxtcout= 5000 xtc-precision= 1000 ; NON BONDED STUFF ns_type = grid nstlist= 5 rlist = 0.8 coulombtype= generalized-reaction-field rcoulomb = 1.4 rvdw = 1.4 epsilon_rf = 54.0 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ; inverse langevin friction cst ref_t= 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = no tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; FREE ENERGY CONTROL STUFF free_energy = yes init_lambda = 0.00 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 ; VELOCITY GENERATION gen_vel = yes gen_temp = 300 gen_seed = -1 -end of prod.mdp I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane (compared to 8.7 in Geerke van Gunsteren, ChemPhysChem 2006, 7, 671 – 678) but I get really huge fluctuations in the values of dg/dl: lambda=0.00: 5.0 +/- 10.8 (mean +/- standard deviation) lambda=0.05: 4.3 +/- 11.2 ... lambda=1.00: -0.3 +/- 4.0 Furthermore, each of these mean value is very slow at converging (1 ns seems a minimum for certain lambda values...). I can't get reasonable fluctuations even if I sample more. In addition, there are very frequent warnings in the log file such as: Large VCM(group rest): 0.01363, 0.00818, 0.01147, ekin-cm: 3.09490e+00 Here are my questions: 1) Has someone an idea of what could be the cause of these [very] large fluctuations? Does it come from my setup, or is this a normal behavior? 2) Are these 'Large VCM(group rest)' warnings related to the use of sd integrator (when I switch to md integrator, I no longer get these warnings) ? Thanks for your answer, Patrick -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] Creation of an index file with seperate lipid leaflets
Hi, I've written a python script that does what you want. I cleaned the script (make_2leaflets_index) and put it on my web page at the following URL: http://condor.ebgm.jussieu.fr/~fuchs/download/index.html Hope it helps. Ciao, Patrick Jay Mashl a écrit : Wasted work would be bad ;) Rather than headgroup orientation, maybe try looking at atom distributions along the bilayer normal direction. Neutron scattering experiments show that for atom groups far from the bilayer midplane, the corresponding z-coordinates form two distinct distributions. So one way could be the following. Pick a headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as input. Search the system by looping over lipids and ask whether that atom type has a z-coordinate within some amount around the input value. From this you know the membership of the leaflets. A more automatic way would be to have the program first discern the distribution and then reread the system to decide the leaflet membership. Jay On Wed, 8 Nov 2006, Alan Dodd wrote: Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl [EMAIL PROTECTED] wrote: On Wed, 8 Nov 2006, Alan Dodd wrote: Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can we calculate chemical shifts
You may also try SHIFTCALC : http://www.shef.ac.uk/NMR/mainframepage.html Patrick David van der Spoel a écrit : Richa taimni wrote: Dear all, my question is that is it possible to calculate chemical shift with the help of gromacs software. You want to get the latest software from the David Case group at Scripps for that. Regards, Richa __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please Help: Still facing problems with installing Gromacs 3.3.1 on SGI Irix
Hi,
I met the same kind of problem with gromacs 3.2.1, and could quickly fix
it, by replacing e.g.
{ evStepOptions[evLINFIX], FALSE, etSTR, {evParams[evLINFIX]}, == {
-linfix, FALSE, etSTR, {evSelections[evLINFIX]}, etc...
See http://www.gromacs.org/pipermail/gmx-users/2004-May/010404.html
Patrick
Akshay Patny a écrit :
SUBJECT: Still facing problems with installing Gromacs 3.3.1 on SGI Irix
Hi
As suggested by Dr. Spoel, I removed one of the semicolons before the
double semicolon in one of the lines in the file gmx_chi.c
I re-installed again and this time it gave me the following error. Can
you suggest what is going wrong and how can I fix it now?
cc-1028 cc: ERROR File = make_edi.c, Line = 579
The expression used must have a constant value.
{ evStepOptions[evLINFIX], FALSE, etSTR, {evParams[evLINFIX]},
^
cc-1028 cc: ERROR File = make_edi.c, Line = 581
The expression used must have a constant value.
{ evStepOptions[evLINACC], FALSE, etSTR, {evParams[evLINACC]},
^
cc-1028 cc: ERROR File = make_edi.c, Line = 583
The expression used must have a constant value.
{ evStepOptions[evRADFIX], FALSE, etREAL, {radfix},
^
cc-1552 cc: WARNING File = make_edi.c, Line = 622
The variable bTop is set but never used.
bool bTop, bM, bFit1;
^
3 errors detected in the compilation of make_edi.c.
*** Error code 2 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
I really appreciate your help.
Kind Regards
Akshay
Akshay Patny
**Akshay Patny***
*
**Graduate Research Assistant**
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Tel: 662-915-1286 (office); Web: www.olemiss.edu http://www.olemiss.edu
___
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--
___
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs
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Re: [gmx-users] Compilation problem on SGI ORIGIN 3800
David van der Spoel a écrit : Patrick Fuchs wrote: Hi gmx users, I'm trying to compile gromacs in // on an SGI ORIGIN 3800. For the monoCPU version it went well (thanks to very good advices on previous E-mails of the gmx list), but for the parallel version, I encountered a problem. Here are the steps I followed : setenv CPPFLAGS -I/opt/mpt/1.4.0.3/usr/include -I/usr/local/include setenv LDFLAGS -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 setenv LIBS -lmpi ./configure --enable-mpi --prefix=/home/fuchs/software/gromacs --program-suffix=_mpi --disable-float --disable-fortran --disable-nice - This step went OK make mdrun - at the beginning it went OK ... (cd ./src/kernel make mdrun ; exit 0) /bin/sh ../../libtool --mode=link mpicc -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -I/usr/freeware/include/libxml2 -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 -woff 84 -o mdrun glaasje.o gctio.o init_sh.o ionize.o do_gct.o relax_sh.o xutils.o md.o mdrun.o genalg.o ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw -lm -lmpi -lXm -lXt -lSM -lICE -lXext -lX11 -L/usr/freeware/lib32 -lxml2 -lz -lm libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.la' was moved. This might be a problem. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw.la' was moved.libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw.la' was moved.libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw.la' was moved. mpicc -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -I/usr/freeware/include/libxml2 -woff 84 -o mdrun glaasje.o gctio.o init_sh.o ionize.o do_gct.o relax_sh.o xutils.o md.o mdrun.o genalg.o -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 ../mdlib/.libs/libmd_mpi_d.a -L/usr/freeware/lib32 ../gmxlib/.libs/libgmx_mpi_d.a -lnsl /usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.a /usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.a /usr/local/lib/fftw2.1.5/lib32/librfftw.a /usr/local/lib/fftw2.1.5/lib32/libfftw.a -lmpi -lXm -lXt -lSM -lICE -lXext -lX11 -lxml2 -lz -lm cc: Warning: -OPT options are ignored cc: Warning: -OPT options are ignored cc: Warning: -SWP options are ignored cc: Warning: -OPT options are ignored uld: Object file format error in: glaasje.o: bad symbolic header (magic number) Something wrong with this file, delete it. *** Error code 1 (bu21) *** Error code 1 (bu21) I didn't find any similar case in the mailing list, and I'm wondering where could it come from. Does someone have an idea on how to fix that ? Thanks ! Patrick Could it be that you have restarted the compilation with differen flags? In that case you will have to do make distclean On SGI machines it has always been a problem to install the compilers, this problem is however hard to distinguish from others. You might want to start from scratch if make distclean doesn't do it. Thank you David, I made a distclean and then used the following : setenv CPPFLAGS -I/opt/mpt/1.4.0.3/usr/include -I/usr/local/include setenv LDFLAGS -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 setenv LIBS -lmpi setenv MPICC cc ./configure --enable-mpi --prefix=/home/fuchs/software/gromacs --program-suffix=_mpi --disable-float --disable-nice make mdrun And it worked ! The thing missing was the line 'setenv MPICC cc', and that makes all the difference. The option --disable-fortran has no effect wether it's used or not, as long as 'setenv MPICC cc' has been set. Ciao, Patrick -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
