Re: [gmx-users] RE: heat capacity etc. (Thomas Koller)
On 2011-03-12 07.52, Thomas Koller wrote: Thanks, the equation for the heat capacity is: c(P) = delta(H(average))/delta(T(average)) So do it have to take the fluctuations (which are listed with g_energy) of U(tot) and pV as well as of T to calculate c(P)? The problem is the delta. The same is with the thermal compressibility: a(P) = 1/V(average) * delta(V(average))/delta(T(average)) Another question: Why should I take U(tot) and not only the potential for c(P)? The same is for the heat of vaporization, here also with U(tot)? Regards, Thomas You need to compute the enthalpy = Etot + pV. The fluctuations in Etot and pV are correlated and compensate each other to some extent, and hence you need to sum the two first and compute the fluctuations afterward. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] versions
On 2011-03-12 08.54, mohsen ramezanpour wrote: Dear All How can I read and work on outputs of one version of Gromacs with tools of other version? Because I have run my program on cluster(version 4.5.3) ,but I need to work with them in v.4.0.7 Suppose I have to work with this version and there is not any way to change versions neighter on cluster no on my laptop Please let me know if there is any solution thanks in advance for your guidances Mohsen you can read xtc and edr from newer version in most of the cases but not tpr. You have to make old tprs. If it is *your* laptop you can upgrade gromacs of course. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] versions
Hi mohsen, I think that I need to work with them in v.4.0.7 means that you need to ANALYZE your trajectory with gmx4.0.7. Is it correct? If this is the case, problem should not arise with trajectory files. You should have problems only with topology that is not back-compatible. However, for the majority of gmx programs, a pdb file that represents your system is sufficient. If you strictly need a .tpr file, I suggest you to create a new topology with the 4.0.7 version. Il 12/03/2011 08:54, mohsen ramezanpour ha scritto: Dear All How can I read and work on outputs of one version of Gromacs with tools of other version? Because I have run my program on cluster(version 4.5.3) ,but I need to work with them in v.4.0.7 Suppose I have to work with this version and there is not any way to change versions neighter on cluster no on my laptop Please let me know if there is any solution thanks in advance for your guidances Mohsen -- 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] versions
thanks for your replies. Yes,you are correct. Actually I need to analyze my trajectories and energy files . I tried but I couldn't use from my energy.edr file in old version(4.0.7),it say: it seems you want to read edr file from version 4.1 or latter with old version Please let me know how can I solve this problem Thanks in advance On Sat, Mar 12, 2011 at 1:38 PM, Francesco Oteri francesco.ot...@gmail.comwrote: Hi mohsen, I think that I need to work with them in v.4.0.7 means that you need to ANALYZE your trajectory with gmx4.0.7. Is it correct? If this is the case, problem should not arise with trajectory files. You should have problems only with topology that is not back-compatible. However, for the majority of gmx programs, a pdb file that represents your system is sufficient. If you strictly need a .tpr file, I suggest you to create a new topology with the 4.0.7 version. Il 12/03/2011 08:54, mohsen ramezanpour ha scritto: Dear All How can I read and work on outputs of one version of Gromacs with tools of other version? Because I have run my program on cluster(version 4.5.3) ,but I need to work with them in v.4.0.7 Suppose I have to work with this version and there is not any way to change versions neighter on cluster no on my laptop Please let me know if there is any solution thanks in advance for your guidances Mohsen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] versions
The exact Error is this: Program g_energy, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/enxio.c, line: 118 Fatal error: You are trying to read an edr file of GROMACS version 4.1 or later with GROMACS version 4.0 On Sat, Mar 12, 2011 at 2:46 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: thanks for your replies. Yes,you are correct. Actually I need to analyze my trajectories and energy files . I tried but I couldn't use from my energy.edr file in old version(4.0.7),it say: it seems you want to read edr file from version 4.1 or latter with old version Please let me know how can I solve this problem Thanks in advance On Sat, Mar 12, 2011 at 1:38 PM, Francesco Oteri francesco.ot...@gmail.com wrote: Hi mohsen, I think that I need to work with them in v.4.0.7 means that you need to ANALYZE your trajectory with gmx4.0.7. Is it correct? If this is the case, problem should not arise with trajectory files. You should have problems only with topology that is not back-compatible. However, for the majority of gmx programs, a pdb file that represents your system is sufficient. If you strictly need a .tpr file, I suggest you to create a new topology with the 4.0.7 version. Il 12/03/2011 08:54, mohsen ramezanpour ha scritto: Dear All How can I read and work on outputs of one version of Gromacs with tools of other version? Because I have run my program on cluster(version 4.5.3) ,but I need to work with them in v.4.0.7 Suppose I have to work with this version and there is not any way to change versions neighter on cluster no on my laptop Please let me know if there is any solution thanks in advance for your guidances Mohsen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding DCCM analysis with g_covar available in user contributed section
Hello, I am using g_covar vailable in user contributed section (by Ran Friedman) the description available for the package is as follows: This package contains a modified version of g_covar, which can print a matrix of atomic correlation coefficients (with -xpmc) and write all pairs with a correlation 0.5 to a log file (with -clog). Otherwise it is the same as the original program. The xpm correlation matrix shows only cross-correlations larger than 0.5 (absolute values) on the upper triangle and all values on the lower triangle. Thus, the upper triangle displays only the most correlated motions. As stated that the upper triangle only shows the cross-correlation greater than 0.5, but I am also getting some negative correlation values(blue regions) in above triangle. I don't know what is the region behind this. Plz help me to understand this behaviour. I have attached my xpm matrix file generated using g_covar. -- * - Thanks and regards Bipin Singh * * * attachment: coor.xpm-- 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] versions
On 2011-03-12 12.23, mohsen ramezanpour wrote: The exact Error is this: Program g_energy, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/enxio.c, line: 118 Fatal error: You are trying to read an edr file of GROMACS version 4.1 or later with GROMACS version 4.0 Upgrade gromacs. On Sat, Mar 12, 2011 at 2:46 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: thanks for your replies. Yes,you are correct. Actually I need to analyze my trajectories and energy files . I tried but I couldn't use from my energy.edr file in old version(4.0.7),it say: it seems you want to read edr file from version 4.1 or latter with old version Please let me know how can I solve this problem Thanks in advance On Sat, Mar 12, 2011 at 1:38 PM, Francesco Oteri francesco.ot...@gmail.com mailto:francesco.ot...@gmail.com wrote: Hi mohsen, I think that I need to work with them in v.4.0.7 means that you need to ANALYZE your trajectory with gmx4.0.7. Is it correct? If this is the case, problem should not arise with trajectory files. You should have problems only with topology that is not back-compatible. However, for the majority of gmx programs, a pdb file that represents your system is sufficient. If you strictly need a .tpr file, I suggest you to create a new topology with the 4.0.7 version. Il 12/03/2011 08:54, mohsen ramezanpour ha scritto: Dear All How can I read and work on outputs of one version of Gromacs with tools of other version? Because I have run my program on cluster(version 4.5.3) ,but I need to work with them in v.4.0.7 Suppose I have to work with this version and there is not any way to change versions neighter on cluster no on my laptop Please let me know if there is any solution thanks in advance for your guidances Mohsen -- 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Questions about implementing G56A_CARB parameters
Hi, I'm about to simulate a disaccaride in water. Reading through the paper from Hansen and Hünenberger: A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. ?Hansen, H. S.; Hünenberger, P. H. /Journal of computational chemistry/. 2010. doi: 10.1002/jcc.21675 it seems like a very rigid work and a good force field to use, since it is directly based on the G53a6 ff already included in gromacs. In the above paper they state that they introduce some things not implemented according to the buildup rules and functionals of the gromos96 program (but part of the upcoming version as of November 2010 though). These things are mainly the ability to use other torsional phase shifts than 0 and 180 degrees and the addition of some 1-3 Lennard-Jones interactions for improved six ring stability. The torsion angle function given in the gromacs manual is exactly the same as they give in the paper above. Thus, my first question is if gromacs have any restrictions on the phase shifts, or if I directly can use the additional shifts of -60 and 60 degrees from 56A_CARB. The second question is about the 1-3 interactions. What's the best way of implementing this? Can I use an nrexcl of 2 and then add the wanted interactions to the pair list and all other to the excluded interactions? Do you have any other suggestions? Best regards Jon Kapla -- 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 gmx change a, b of 3D pbc box but remain c in constant-NPT MD?
英雄不再寂寞 wrote: Dear gmxers, I want to perform a constant-NPT MD simulation using gmx. By default, a,b,c of 3D pbc box can change to compatile with the density. Whether can gmx change a,b of 3D pbc box but unchange c? Please give me some hints. Thanks a lot. Set the compressibility of whichever direction you need to be constant to zero. This would require anisotropic or semi-isotropic coupling to allow other dimensions to scale. -Justin Yours sincerely, Chaofu Wu, Dr. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Possible free energy bug?
Hi All, I believe I have a resolution to all of this. It comes down to compilers and FFTW. I had always used the same compilers to build all my Gromacs versions (gcc-4.2.2 on Linux, gcc-3.3 on OSX) with the same version of FFTW (3.0.1), primarily for reasons of continuity. Bug 715 that I posted before was due to a problem with FFTW, not Gromacs; upgrading to 3.2.2 solves the issue. As well, the combination of gcc-4.4.5 + FFTW 3.2.2 allows for successful free energy runs in my tests thus far on Linux. Dependency issues on the OS X partition prevent me from doing any upgrades, so we're out of luck there, unfortunately. I will report back if any other weird behavior results, but I believe the problem is solved. I am no compiler/library guru, but it would seem to me that we've reached a point where certain minimum versions must be required for certain prerequisites. I would suggest that prior to the next release, we come up with a list of what should be considered stable minimum requirements (compiler versions, FFTW, anything else) to post on the website and perhaps the manual. As it stands now, the prerequisites for installation would seem to be satisfied by any C compiler and any version of FFTW. Gromacs happily compiles under most conditions, but shows some weird behavior if one is not using optimal dependencies. Thanks to all for their input! -Justin Justin A. Lemkul wrote: Michael Shirts wrote: Hi, all- Have you tried running constraints = hbonds? That might eliminate some of the constraint issues. Much less likely for LINCS to break or have DD issues if only the hbonds are constrained. 2 fs is not that big a deal for the heteroatom bonds. I haven't yet, but I'll add it to my to-do list. I was trying to keep as many things consistent between my 3.3.3 and 4.5.3 input files as possible, so I could diagnose any issues, but at this point, anything is worth a shot. Thanks! -Justin Best, Michael On Thu, Mar 10, 2011 at 8:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Hi Matt, Thanks for the extensive explanation and tips. I'll work through things and report back. It will take a while to get things going through (unless one of the early solutions works!) since I have no admin access to install new compilers, libraries, etc. and for some reason the only thing I can ever get to work in my home directory is Gromacs itself. The joys of an aging cluster. We recently got access to gcc-4.4.5 on Linux, but we're stuck with 3.3 on OS X, so there's at least a bit of hope for one partition. Thanks again. -Justin Matthew Zwier wrote: Hi Justin, I should have specified that the segfault happened for us after we got similar warnings and errors (DD and/or LINCS), so the segfault may have been tangential. Given that everything about your system worked before GROMACS 4.5, it's possible that your older compilers are generating code that's incompatible with the GROMACS assembly loops (which you are likely running with, as they are the default option on most mainstream processors). The bug you mentioned in your original post also has my antennae twitching about bad machine code. If that's indeed happening, it's almost certainly some bizarre alignment issue, something like half of a float is getting overwritten on the way into or out of the assembly code, which corruption would trigger the results you describe. It's also distantly possible that GROMACS is working fine, but your copy of FFTW or BLAS/LAPACK (more likely the latter) has alignment problems. One final possibility (which would explain the failure on YellowDog but unfortunately not the failure on OS X) is that GCC is generating badly-aligned code for auto-vectorized Altivec loops, which is still a problem for Intel's SIMD instructions on 32-bit x86 architectures even with GCC 4.4. I've also observed MPI gather/reduce operations to foul up alignment (or rigidly enforce it where badly compiled code is relying on broken alignment) under exceedingly rare circumstances, usually involving different libraries compiled with different compilers (which is generally a bad idea for scientific code anyway). Okay...so all of that said, there are a few things to try: 1) Recompile GROMACS using -O2 instead of -O3; that'll turn off the automatic vectorizer (on Yellow Dog) and various other relatively risky optimizations (on both platforms). CFLAGS=-O2 -march=powerpc in the environment AND on the configure command line would do that. Check your build logs to make sure it took, though, because if you don't do it exactly right, configure will ignore your directives and merrily set up GROMACS to compile with -O3, which is the most likely culprit for badly-aligned code. 2) Recompile GROMACS specifying a forced alignment flag. I have no experience with PowerPC, but -malign-natural and -malign-power look like good initial guesses. That's probably going to cause more problems than it solves, but if you have a
[gmx-users] RE: Regarding DCCM analysis with g_covar available in user contributed section
Hi, As stated below the upper half of the triangle shows correlations having r0.5 or r-0.5, that is |r|0.5 Ran From: bipin singh [bipinel...@gmail.com] Sent: 12 March 2011 12:27 To: Discussion list for GROMACS users Cc: r.fried...@bioc.uzh.ch Subject: Regarding DCCM analysis with g_covar available in user contributed section Hello, I am using g_covar vailable in user contributed section (by Ran Friedman) the description available for the package is as follows: This package contains a modified version of g_covar, which can print a matrix of atomic correlation coefficients (with -xpmc) and write all pairs with a correlation 0.5 to a log file (with -clog). Otherwise it is the same as the original program. The xpm correlation matrix shows only cross-correlations larger than 0.5 (absolute values) on the upper triangle and all values on the lower triangle. Thus, the upper triangle displays only the most correlated motions. As stated that the upper triangle only shows the cross-correlation greater than 0.5, but I am also getting some negative correlation values(blue regions) in above triangle. I don't know what is the region behind this. Plz help me to understand this behaviour. I have attached my xpm matrix file generated using g_covar. -- - Thanks and regards Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: heat capacity etc. (Thomas Koller)
I dont know exactly what you mean. Here you can see my output data: Energy AverageRMSDFluct. Drift Tot-Drift --- Potential -48.8499 1.82144 1.81841 -0.00781553 -0.3638 Kinetic En.50.7548 1.42996 1.42991 -0.000872827 -0.0406286 Total Energy 1.90489 2.32653 2.3236 -0.00868836 -0.404429 Temperature298.15 8.40003 8.39975 -8.84014e-05 -0.238666 Pressure (bar) 1.66395 713.24 713.236 0.00302056 8.15491 Volume 21.0391 0.179301 0.178412-2.2873e-05 -0.0617527 pV-0.45227 903.541 903.536 0.00377916 10.203 Heat Capacity Cv: 13.3969 J/mol K (factor = 0.0460384) Isothermal Compressibility: 3.71208e-05 /bar Adiabatic bulk modulus:26939.1 bar i) How should I calculate the isobaric heat capacity with this values, bu udage of the Fluct. in the 3rd column? ii) How is the isothermal compressibility here calculated? Regards, Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- 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] Surface tension readings in NVT vs NPT simulations
David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] versions
That are different way: 1. Performing analysis directly on the cluster where 4.5.3 is installed 2. Installing gmx 4.5.3 on you laptop. 3. Writing a program that converts from 4.5.3 to 4.0.7 Il 12/03/2011 12:16, mohsen ramezanpour ha scritto: thanks for your replies. Yes,you are correct. Actually I need to analyze my trajectories and energy files . I tried but I couldn't use from my energy.edr file in old version(4.0.7),it say: it seems you want to read edr file from version 4.1 or latter with old version Please let me know how can I solve this problem Thanks in advance On Sat, Mar 12, 2011 at 1:38 PM, Francesco Oteri francesco.ot...@gmail.com mailto:francesco.ot...@gmail.com wrote: Hi mohsen, I think that I need to work with them in v.4.0.7 means that you need to ANALYZE your trajectory with gmx4.0.7. Is it correct? If this is the case, problem should not arise with trajectory files. You should have problems only with topology that is not back-compatible. However, for the majority of gmx programs, a pdb file that represents your system is sufficient. If you strictly need a .tpr file, I suggest you to create a new topology with the 4.0.7 version. Il 12/03/2011 08:54, mohsen ramezanpour ha scritto: Dear All How can I read and work on outputs of one version of Gromacs with tools of other version? Because I have run my program on cluster(version 4.5.3) ,but I need to work with them in v.4.0.7 Suppose I have to work with this version and there is not any way to change versions neighter on cluster no on my laptop Please let me know if there is any solution thanks in advance for your guidances Mohsen -- 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: heat capacity etc. (Thomas Koller)
On 2011-03-12 14.00, Thomas Koller wrote: I dont know exactly what you mean. Here you can see my output data: Energy AverageRMSDFluct. Drift Tot-Drift --- Potential -48.8499 1.82144 1.81841 -0.00781553 -0.3638 Kinetic En.50.7548 1.42996 1.42991 -0.000872827 -0.0406286 Total Energy 1.90489 2.32653 2.3236 -0.00868836 -0.404429 Temperature298.15 8.40003 8.39975 -8.84014e-05 -0.238666 Pressure (bar) 1.66395 713.24 713.236 0.00302056 8.15491 Volume 21.0391 0.179301 0.178412-2.2873e-05 -0.0617527 pV-0.45227 903.541 903.536 0.00377916 10.203 Heat Capacity Cv: 13.3969 J/mol K (factor = 0.0460384) Isothermal Compressibility: 3.71208e-05 /bar Adiabatic bulk modulus:26939.1 bar i) How should I calculate the isobaric heat capacity with this values, bu udage of the Fluct. in the 3rd column? ii) How is the isothermal compressibility here calculated? Regards, Thomas You have to read up, check Allen Tildesly or something like that. To get the enthalpy you have to extract the total energy graph and and the volume graph and sum Etot + p time Volume (in xmgrace or excel, whatever). Then compute the fluctuations from that. You have to do it all manually. The heat capacity above is meaningless, this is why we have improved that in newer gmx version. Note that if you have used Berendsen T and/or P coupling you can not compute any fluctuation properties from your simulations. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjorder, what and how does es count (amount solvent atoms or molecules)?
Dear Gromacs Users, I'm using trjorder with the following options: $ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r 0.35 -nshell system0.35.nshell.xvg As the first group I select all the atoms of a single TYR residue, which is part of a larger protein. As the second group I select all the solvent atoms (TIP3P). For a radius of 3.5 A I observe in most frames the number 8, the observations range from 0 to even 20. What does this number mean exactly? For TIP3P the OH2-H1 and OH2-H2 distance is approx. 1A and the H1 and H2 distance is approx. 1.6A. This gives a volume of 4.2A^3 for TIP3P. A sphere of 3.5A would have a volume of 14.6A^3. As a first order approximation this would suggest for non buried TYR residue about 3 to 4 TIP3P molecules which could fit in this sphere. This differs from the number 8 which trjorder measures. My questions are: 1. What does trajorder count? Does it count the number of solvent atoms or of solvent molecules? 2. How does trajorder count? If trajorder counts the amount of molecules. Is it sufficient that a single atom of the molecules is in the sphere to be included in the counting or must all atoms of the molecule be in the sphere to be included in the counting? Thanks, Henri -- 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] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
Re: [gmx-users] trjorder, what and how does es count (amount solvent atoms or molecules)?
Henri Mone wrote: Dear Gromacs Users, I'm using trjorder with the following options: $ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r 0.35 -nshell system0.35.nshell.xvg As the first group I select all the atoms of a single TYR residue, which is part of a larger protein. As the second group I select all the solvent atoms (TIP3P). For a radius of 3.5 A I observe in most frames the number 8, the observations range from 0 to even 20. What does this number mean exactly? For TIP3P the OH2-H1 and OH2-H2 distance is approx. 1A and the H1 and H2 distance is approx. 1.6A. This gives a volume of 4.2A^3 for TIP3P. A sphere of 3.5A would have a volume of 14.6A^3. As a first order approximation this would suggest for non buried TYR residue about 3 to 4 TIP3P molecules which could fit in this sphere. This differs from the number 8 which trjorder measures. My questions are: 1. What does trajorder count? Does it count the number of solvent atoms or of solvent molecules? trjorder -h: With option -nshell the number of molecules within a shell of radius -r around the reference group are printed. 2. How does trajorder count? If trajorder counts the amount of molecules. Is it sufficient that a single atom of the molecules is in the sphere to be included in the counting or must all atoms of the molecule be in the sphere to be included in the counting? Check the code. If nothing else, your approximation is off. Would a sphere of 0.35 nm completely encompass your whole Tyr residue? The distance are presumably based on a radius of 0.35 nm of each of the constituent atoms, making for a somewhat larger effective volume. -Justin Thanks, Henri -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 16.59, Denny Frost wrote: Is that using anisotropic pressure coupling? yes. just try it On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 17.28, Denny Frost wrote: No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? with semiisotropic you need only two values, with anisotropic either 3 or 6 values. Zero compressibility should work. On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
It won't take zero with the berendsen thermostat, but I only wish to do weak coupling for now. Yes, I only specified the two values for semiisotropic. What I'm asking is will this setup only do z-pressure coupling? On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 17.28, Denny Frost wrote: No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? with semiisotropic you need only two values, with anisotropic either 3 or 6 values. Zero compressibility should work. On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as
RE: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Based on a preliminary test using multiple threads, the issue is not resolved. This leads me to believe that my Unit Cell is not built properly. Below is the procedure used to build the unit cell. I have reviewed it many times, but I would appreciate any input regarding potential improvements, specifically on the line using trjconv in the EM/Shrink loop. Safe up to here, (I hope)... cat KALP_newbox.gro dppc128_whole.gro system.gro update minim.mdp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif Create Strong Position Restraint for protein genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Scale Lipid positions by a factor of 4 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Begin loop of repeated Energy Minimizations and Shrinking (repeat loop approximately 25 times until area is approx 71 Ang sq) Begin LOOP (from n=1 to n = 26) grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr mdrun -v -deffnm em_n trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5 ar_shr1.dat End LOOP Add water Add ions Re-run EM Equilibrate (and watch it all explode) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, March 10, 2011 12:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian wrote: On 03/08/2011 10:23 PM, Justin A. Lemkul wrote: Steve Vivian wrote: New to Gromacs. Worked my way through the tutorial with relatively few issues until the Equilibration stage. My system blows up!! Returned to the Topology stage and rebuilt my system ensuring that I followed the procedure correctly for the InflateGro process. It appears to be correct, reasonable lipid area, no water inside my bilayer, vmd shows a structure which appears normal (although I am new to this). There are voids between bilayer and water molecules, but this is to be expected, correct? Energy Minimization repeatedly produces results within the expected range. Again system blows up at equilibration, step 0 segmentation fault. Regardless of whether I attempt the NVT or Anneal_Npt process (using the provided mdp files, including the updates for restraints on the protein and the lipid molecules). I have attempted many variations of the nvt.mdp and anneal_npt.mdp files hoping to resolve my issue, but with no success. I will post the log information from the nvt.mdp file included in the tutorial. Started mdrun on node 0 Tue Mar 8 15:42:35 2011 Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.52380e+016.88116e+012.23939e+01 -3.03546e+012.71260e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 1.49883e+04 -1.42684e+03 -2.78329e+05 -1.58540e+052.57100e+00 PotentialKinetic En. Total Energy Conserved En. Temperature -4.20446e+05*1.41436e+141.41436e+14 1.41436e+141.23343e+12* Pres. DC (bar) Pressure (bar) Constr. rmsd -1.56331e+025.05645e+121.18070e+01 As you can see the Potential Energy is reasonable, but the Kinetic Energy and Temperature seem unrealistic. I am hoping that this is enough information for a more experienced Gromacs user to provide guidance. Note: that I have tried all of the suggestions that I read on the mailing list and in the blowing up section of the manual, specifically: -reduced time steps in Equilibration Stages -reduced Fmax during EM stage (down as low as 100kJ which did not help) -modified neighbours list parameters Any help is appreciated. I can attach and forward any further information as required, please let me know. Which Gromacs version are you using? It looks like you're running in serial, is that correct? Otherwise, please provide your mdrun command line. If you're using version 4.5.3 in serial, I have identified a very problematic bug that seems to affect a wide variety of systems that could be related: Yes I am currently using Gromacs 4.5.3 in serial. http://redmine.gromacs.org/issues/715 I have seen even the most robust tutorial systems fail as well, as some new lab members experienced the same problem. The workaround is to run in parallel. If I understand you correctly, the recommended workaround is to re-configure gromacs 4.5.3 with mpi enabled and complete the Equilibration and
Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Steve Vivian wrote: Based on a preliminary test using multiple threads, the issue is not resolved. This leads me to believe that my Unit Cell is not built properly. Below is the procedure used to build the unit cell. I have reviewed it many times, but I would appreciate any input regarding potential improvements, specifically on the line using trjconv in the EM/Shrink loop. Safe up to here, (I hope)... cat KALP_newbox.gro dppc128_whole.gro system.gro update minim.mdp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif Create Strong Position Restraint for protein genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Scale Lipid positions by a factor of 4 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Begin loop of repeated Energy Minimizations and Shrinking (repeat loop approximately 25 times until area is approx 71 Ang sq) Begin LOOP (from n=1 to n = 26) grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr mdrun -v -deffnm em_n trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5 ar_shr1.dat End LOOP Add water Add ions Re-run EM What is the outcome of EM? -Justin Equilibrate (and watch it all explode) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, March 10, 2011 12:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian wrote: On 03/08/2011 10:23 PM, Justin A. Lemkul wrote: Steve Vivian wrote: New to Gromacs. Worked my way through the tutorial with relatively few issues until the Equilibration stage. My system blows up!! Returned to the Topology stage and rebuilt my system ensuring that I followed the procedure correctly for the InflateGro process. It appears to be correct, reasonable lipid area, no water inside my bilayer, vmd shows a structure which appears normal (although I am new to this). There are voids between bilayer and water molecules, but this is to be expected, correct? Energy Minimization repeatedly produces results within the expected range. Again system blows up at equilibration, step 0 segmentation fault. Regardless of whether I attempt the NVT or Anneal_Npt process (using the provided mdp files, including the updates for restraints on the protein and the lipid molecules). I have attempted many variations of the nvt.mdp and anneal_npt.mdp files hoping to resolve my issue, but with no success. I will post the log information from the nvt.mdp file included in the tutorial. Started mdrun on node 0 Tue Mar 8 15:42:35 2011 Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.52380e+016.88116e+012.23939e+01 -3.03546e+012.71260e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 1.49883e+04 -1.42684e+03 -2.78329e+05 -1.58540e+052.57100e+00 PotentialKinetic En. Total Energy Conserved En. Temperature -4.20446e+05*1.41436e+141.41436e+14 1.41436e+141.23343e+12* Pres. DC (bar) Pressure (bar) Constr. rmsd -1.56331e+025.05645e+121.18070e+01 As you can see the Potential Energy is reasonable, but the Kinetic Energy and Temperature seem unrealistic. I am hoping that this is enough information for a more experienced Gromacs user to provide guidance. Note: that I have tried all of the suggestions that I read on the mailing list and in the blowing up section of the manual, specifically: -reduced time steps in Equilibration Stages -reduced Fmax during EM stage (down as low as 100kJ which did not help) -modified neighbours list parameters Any help is appreciated. I can attach and forward any further information as required, please let me know. Which Gromacs version are you using? It looks like you're running in serial, is that correct? Otherwise, please provide your mdrun command line. If you're using version 4.5.3 in serial, I have identified a very problematic bug that seems to affect a wide variety of systems that could be related: Yes I am currently using Gromacs 4.5.3 in serial. http://redmine.gromacs.org/issues/715 I have seen even the most robust tutorial systems fail as well, as some new lab members experienced the same problem. The workaround is to run in parallel. If I understand you correctly, the recommended workaround is to re-configure gromacs 4.5.3 with mpi enabled and complete the
Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Steve Vivian wrote: Based on a preliminary test using multiple threads, the issue is not resolved. This leads me to believe that my Unit Cell is not built properly. Below is the procedure used to build the unit cell. I have reviewed it many times, but I would appreciate any input regarding potential improvements, specifically on the line using trjconv in the EM/Shrink loop. Safe up to here, (I hope)... cat KALP_newbox.gro dppc128_whole.gro system.gro update minim.mdp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif Create Strong Position Restraint for protein genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Scale Lipid positions by a factor of 4 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Begin loop of repeated Energy Minimizations and Shrinking (repeat loop approximately 25 times until area is approx 71 Ang sq) Begin LOOP (from n=1 to n = 26) grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr mdrun -v -deffnm em_n trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5 One problem here: you start the loop every time with system_inf_n? What is system_inf_n? It seems that you should start one (non-loop) shrink and then process the subsequent shrinking steps from there. At the end of the loop, you write to sys_shr_1.gro, which then never gets used again. -Justin ar_shr1.dat End LOOP Add water Add ions Re-run EM Equilibrate (and watch it all explode) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, March 10, 2011 12:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian wrote: On 03/08/2011 10:23 PM, Justin A. Lemkul wrote: Steve Vivian wrote: New to Gromacs. Worked my way through the tutorial with relatively few issues until the Equilibration stage. My system blows up!! Returned to the Topology stage and rebuilt my system ensuring that I followed the procedure correctly for the InflateGro process. It appears to be correct, reasonable lipid area, no water inside my bilayer, vmd shows a structure which appears normal (although I am new to this). There are voids between bilayer and water molecules, but this is to be expected, correct? Energy Minimization repeatedly produces results within the expected range. Again system blows up at equilibration, step 0 segmentation fault. Regardless of whether I attempt the NVT or Anneal_Npt process (using the provided mdp files, including the updates for restraints on the protein and the lipid molecules). I have attempted many variations of the nvt.mdp and anneal_npt.mdp files hoping to resolve my issue, but with no success. I will post the log information from the nvt.mdp file included in the tutorial. Started mdrun on node 0 Tue Mar 8 15:42:35 2011 Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.52380e+016.88116e+012.23939e+01 -3.03546e+012.71260e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 1.49883e+04 -1.42684e+03 -2.78329e+05 -1.58540e+052.57100e+00 PotentialKinetic En. Total Energy Conserved En. Temperature -4.20446e+05*1.41436e+141.41436e+14 1.41436e+141.23343e+12* Pres. DC (bar) Pressure (bar) Constr. rmsd -1.56331e+025.05645e+121.18070e+01 As you can see the Potential Energy is reasonable, but the Kinetic Energy and Temperature seem unrealistic. I am hoping that this is enough information for a more experienced Gromacs user to provide guidance. Note: that I have tried all of the suggestions that I read on the mailing list and in the blowing up section of the manual, specifically: -reduced time steps in Equilibration Stages -reduced Fmax during EM stage (down as low as 100kJ which did not help) -modified neighbours list parameters Any help is appreciated. I can attach and forward any further information as required, please let me know. Which Gromacs version are you using? It looks like you're running in serial, is that correct? Otherwise, please provide your mdrun command line. If you're using version 4.5.3 in serial, I have identified a very problematic bug that seems to affect a wide variety of systems that could be related: Yes I am currently using Gromacs 4.5.3 in serial. http://redmine.gromacs.org/issues/715 I have seen even the most
Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
On 03/12/2011 12:51 PM, Justin A. Lemkul wrote: Getting hard to follow, so I put my new comments in blue. Output from Energy Minimization Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 Steve Vivian wrote: Based on a preliminary test using multiple threads, the issue is not resolved. This leads me to believe that my Unit Cell is not built properly. Below is the procedure used to build the unit cell. I have reviewed it many times, but I would appreciate any input regarding potential improvements, specifically on the line using trjconv in the EM/Shrink loop. Safe up to here, (I hope)... cat KALP_newbox.gro dppc128_whole.gro system.gro update minim.mdp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif Create Strong Position Restraint for protein genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Scale Lipid positions by a factor of 4 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Begin loop of repeated Energy Minimizations and Shrinking (repeat loop approximately 25 times until area is approx 71 Ang sq) Begin LOOP (from n=1 to n = 26) grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr mdrun -v -deffnm em_n trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5 One problem here: you start the loop every time with system_inf_n? What is system_inf_n? It seems that you should start one (non-loop) shrink and then process the subsequent shrinking steps from there. At the end of the loop, you write to sys_shr_1.gro, which then never gets used again. -Justin Put my comments in blue to make it easier to read. I apologize for the poor description here. The first loop begins with the System_inflate.gro file created in the earlier process. The rest of the first loop is shown. At the beginning of the second loop, the input file is system_shrink_1.gro, which was the output file at the end of loop 1. Proceed through the loop, updating the n from 1 to 2 in each step. Output file is system_shrink_2.gro. Input file for loop 3 is system_shrink_3.gro, Output from loop 26 is system_shrink_26.gro and output on screen provides information on updated Lipid area which has achieved target value. Then proceed to add water (after changing vdw radius of C atoms) Add ions EM again Then Equilibrate. Output from Energy Minimization (after addition of water and ions) Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 ar_shr1.dat End LOOP Add water Add ions Re-run EM Equilibrate (and watch it all explode) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, March 10, 2011 12:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian wrote: On 03/08/2011 10:23 PM, Justin A. Lemkul wrote: Steve Vivian wrote: New to Gromacs. Worked my way through the tutorial with relatively few issues until the Equilibration stage. My system blows up!! Returned to the Topology stage and rebuilt my system ensuring that I followed the procedure correctly for the InflateGro process. It appears to be correct, reasonable lipid area, no water inside my bilayer, vmd shows a structure which appears normal (although I am new to this). There are voids between bilayer and water molecules, but this is to be expected, correct? Energy Minimization repeatedly produces results within the expected range. Again system blows up at equilibration, step 0 segmentation fault. Regardless of whether I attempt the NVT or Anneal_Npt process (using the provided mdp files, including the updates for restraints on the protein and the lipid molecules). I have attempted many variations of the nvt.mdp and anneal_npt.mdp files hoping to resolve my issue, but with no success. I will post the log information from the nvt.mdp file included in the tutorial. Started mdrun on node 0 Tue Mar 8 15:42:35 2011 Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.52380e+016.88116e+012.23939e+01 -3.03546e+012.71260e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 1.49883e+04 -1.42684e+03 -2.78329e+05 -1.58540e+052.57100e+00 Potential
Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Steve Vivian wrote: On 03/12/2011 12:51 PM, Justin A. Lemkul wrote: Getting hard to follow, so I put my new comments in blue. Output from Energy Minimization Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 Steve Vivian wrote: Based on a preliminary test using multiple threads, the issue is not resolved. This leads me to believe that my Unit Cell is not built properly. Below is the procedure used to build the unit cell. I have reviewed it many times, but I would appreciate any input regarding potential improvements, specifically on the line using trjconv in the EM/Shrink loop. Safe up to here, (I hope)... cat KALP_newbox.gro dppc128_whole.gro system.gro update minim.mdp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif Create Strong Position Restraint for protein genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Scale Lipid positions by a factor of 4 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Begin loop of repeated Energy Minimizations and Shrinking (repeat loop approximately 25 times until area is approx 71 Ang sq) Begin LOOP (from n=1 to n = 26) grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr mdrun -v -deffnm em_n trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5 One problem here: you start the loop every time with system_inf_n? What is system_inf_n? It seems that you should start one (non-loop) shrink and then process the subsequent shrinking steps from there. At the end of the loop, you write to sys_shr_1.gro, which then never gets used again. -Justin Put my comments in blue to make it easier to read. I apologize for the poor description here. The first loop begins with the System_inflate.gro file created in the earlier process. The rest of the first loop is shown. At the beginning of the second loop, the input file is system_shrink_1.gro, which was the output file at the end of loop 1. Proceed through the loop, updating the n from 1 to 2 in each step. Output file is system_shrink_2.gro. Input file for loop 3 is system_shrink_3.gro, Output from loop 26 is system_shrink_26.gro and output on screen provides information on updated Lipid area which has achieved target value. Then proceed to add water (after changing vdw radius of C atoms) Add ions EM again Then Equilibrate. Output from Energy Minimization (after addition of water and ions) Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 This output indicates to me that the system is completely reasonable. If you send me your .gro and .top (off-list), I will try to debug and report back if I can find anything. To confirm, you are using Gromacs 4.5.3? What version of FFTW? What hardware? What compilers were used for the installation? -Justin ar_shr1.dat End LOOP Add water Add ions Re-run EM Equilibrate (and watch it all explode) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, March 10, 2011 12:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian wrote: On 03/08/2011 10:23 PM, Justin A. Lemkul wrote: Steve Vivian wrote: New to Gromacs. Worked my way through the tutorial with relatively few issues until the Equilibration stage. My system blows up!! Returned to the Topology stage and rebuilt my system ensuring that I followed the procedure correctly for the InflateGro process. It appears to be correct, reasonable lipid area, no water inside my bilayer, vmd shows a structure which appears normal (although I am new to this). There are voids between bilayer and water molecules, but this is to be expected, correct? Energy Minimization repeatedly produces results within the expected range. Again system blows up at equilibration, step 0 segmentation fault. Regardless of whether I attempt the NVT or Anneal_Npt process (using the provided mdp files, including the updates for restraints on the protein and the lipid molecules). I have attempted many variations of the nvt.mdp and anneal_npt.mdp files hoping to resolve my issue, but with no success. I will post the log information from the nvt.mdp file included in the tutorial. Started mdrun on node 0 Tue Mar 8 15:42:35 2011 Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Energies (kJ/mol) G96AngleProper Dih. Improper
Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Steve Vivian wrote: On 03/12/2011 01:36 PM, Justin A. Lemkul wrote: Steve Vivian wrote: On 03/12/2011 12:51 PM, Justin A. Lemkul wrote: Getting hard to follow, so I put my new comments in blue. Output from Energy Minimization Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 Steve Vivian wrote: Based on a preliminary test using multiple threads, the issue is not resolved. This leads me to believe that my Unit Cell is not built properly. Below is the procedure used to build the unit cell. I have reviewed it many times, but I would appreciate any input regarding potential improvements, specifically on the line using trjconv in the EM/Shrink loop. Safe up to here, (I hope)... cat KALP_newbox.gro dppc128_whole.gro system.gro update minim.mdp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif Create Strong Position Restraint for protein genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Scale Lipid positions by a factor of 4 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Begin loop of repeated Energy Minimizations and Shrinking (repeat loop approximately 25 times until area is approx 71 Ang sq) Begin LOOP (from n=1 to n = 26) grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr mdrun -v -deffnm em_n trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5 One problem here: you start the loop every time with system_inf_n? What is system_inf_n? It seems that you should start one (non-loop) shrink and then process the subsequent shrinking steps from there. At the end of the loop, you write to sys_shr_1.gro, which then never gets used again. -Justin Put my comments in blue to make it easier to read. I apologize for the poor description here. The first loop begins with the System_inflate.gro file created in the earlier process. The rest of the first loop is shown. At the beginning of the second loop, the input file is system_shrink_1.gro, which was the output file at the end of loop 1. Proceed through the loop, updating the n from 1 to 2 in each step. Output file is system_shrink_2.gro. Input file for loop 3 is system_shrink_3.gro, Output from loop 26 is system_shrink_26.gro and output on screen provides information on updated Lipid area which has achieved target value. Then proceed to add water (after changing vdw radius of C atoms) Add ions EM again Then Equilibrate. Output from Energy Minimization (after addition of water and ions) Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 This output indicates to me that the system is completely reasonable. If you send me your .gro and .top (off-list), I will try to debug and report back if I can find anything. To confirm, you are using Gromacs 4.5.3? What version of FFTW? What hardware? What compilers were used for the installation? -Justin Using Gromacs 4.5.3 and FFTW 3.2.2 both compiled for double precision. It has been a while since I compiled so I'm not exactly sure, but I recall updating gcc and gfortran during the process. Hardware, what type of specifics are you looking for? # of processors and speed? Attached are current Energy Minimized file and topology file. Hardware and compiler specs are unnecessary. The problem is the coordinate file itself. Look at it in your favorite visualization program and you will see that the lipid headgroups are completely collapsed in on one another. I don't know how or why this happened. If you're using the DPPC topology from Tieleman and the .mdp files given in the tutorial, I see no reason for this totally unstable configuration. I have never used double precision (and it is not necessary for standard MD, and only serves to slow your runs down), so it would be interesting to see if the problem is a result of double vs. single precision. I can successfully re-minimize the coordinate file you sent me using single precision: Steepest Descents converged to Fmax 1000 in 335 steps Potential Energy = -6.3605750e+04 Maximum force = 7.1865680e+02 on atom 115 Norm of force = 3.9649860e+01 For now, I would suggest you test the precision issue. Install Gromacs again (making note of your compiler versions, because this is important to know!) in single precision and try to re-minimize the system and proceed. No need to completely re-build it, as you should be able to just run a new EM on your existing system like I did. -Justin Steve. ar_shr1.dat End LOOP Add water Add ions Re-run EM Equilibrate (and watch it all
[gmx-users] terminated but not completely
Dear All I run a simulation for 4 days. Unfortunately it terminated,but not completely,1 steps from 2 has done. Is there any way to run the continue of my files? Thanks in advance for your guidances Best Regards -- 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] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
On 03/12/2011 02:10 PM, Justin A. Lemkul wrote: Steve Vivian wrote: On 03/12/2011 01:36 PM, Justin A. Lemkul wrote: Steve Vivian wrote: On 03/12/2011 12:51 PM, Justin A. Lemkul wrote: Getting hard to follow, so I put my new comments in blue. Output from Energy Minimization Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 Steve Vivian wrote: Based on a preliminary test using multiple threads, the issue is not resolved. This leads me to believe that my Unit Cell is not built properly. Below is the procedure used to build the unit cell. I have reviewed it many times, but I would appreciate any input regarding potential improvements, specifically on the line using trjconv in the EM/Shrink loop. Safe up to here, (I hope)... cat KALP_newbox.gro dppc128_whole.gro system.gro update minim.mdp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif Create Strong Position Restraint for protein genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Scale Lipid positions by a factor of 4 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Begin loop of repeated Energy Minimizations and Shrinking (repeat loop approximately 25 times until area is approx 71 Ang sq) Begin LOOP (from n=1 to n = 26) grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr mdrun -v -deffnm em_n trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5 One problem here: you start the loop every time with system_inf_n? What is system_inf_n? It seems that you should start one (non-loop) shrink and then process the subsequent shrinking steps from there. At the end of the loop, you write to sys_shr_1.gro, which then never gets used again. -Justin Put my comments in blue to make it easier to read. I apologize for the poor description here. The first loop begins with the System_inflate.gro file created in the earlier process. The rest of the first loop is shown. At the beginning of the second loop, the input file is system_shrink_1.gro, which was the output file at the end of loop 1. Proceed through the loop, updating the n from 1 to 2 in each step. Output file is system_shrink_2.gro. Input file for loop 3 is system_shrink_3.gro, Output from loop 26 is system_shrink_26.gro and output on screen provides information on updated Lipid area which has achieved target value. Then proceed to add water (after changing vdw radius of C atoms) Add ions EM again Then Equilibrate. Output from Energy Minimization (after addition of water and ions) Steepest Descents converged to Fmax 1000 in 1814 steps Potential Energy = -3.81270276926664e+05 Maximum force = 9.38712770623942e+02 on atom 2292 Norm of force = 2.88274347161761e+01 This output indicates to me that the system is completely reasonable. If you send me your .gro and .top (off-list), I will try to debug and report back if I can find anything. To confirm, you are using Gromacs 4.5.3? What version of FFTW? What hardware? What compilers were used for the installation? -Justin Using Gromacs 4.5.3 and FFTW 3.2.2 both compiled for double precision. It has been a while since I compiled so I'm not exactly sure, but I recall updating gcc and gfortran during the process. Hardware, what type of specifics are you looking for? # of processors and speed? Attached are current Energy Minimized file and topology file. Hardware and compiler specs are unnecessary. The problem is the coordinate file itself. Look at it in your favorite visualization program and you will see that the lipid headgroups are completely collapsed in on one another. I don't know how or why this happened. If you're using the DPPC topology from Tieleman and the .mdp files given in the tutorial, I see no reason for this totally unstable configuration. I have never used double precision (and it is not necessary for standard MD, and only serves to slow your runs down), so it would be interesting to see if the problem is a result of double vs. single precision. I can successfully re-minimize the coordinate file you sent me using single precision: Steepest Descents converged to Fmax 1000 in 335 steps Potential Energy = -6.3605750e+04 Maximum force = 7.1865680e+02 on atom 115 Norm of force = 3.9649860e+01 For now, I would suggest you test the precision issue. Install Gromacs again (making note of your compiler versions, because this is important to know!) in single precision and try to re-minimize the system and proceed. No need to completely re-build it, as you should be able to just run a new EM on your existing system like I did. -Justin Questions regarding re-compiling FFTW and Gromacs
Re: [gmx-users] Possible free energy bug? (NOT SOLVED)
Hi All,
Unfortunately, my positive news was a false alarm. Intermediate values of
lambda are sporadically failing at different times. Some jobs exit at time
zero, others last somewhat longer (several hundred ps) before failing. I'm
going to keep working on the suggestions I got before about compilation options
and such, but for now I will post the error output to see if it provides any
clues about what's wrong:
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
[n921:01432] *** Process received signal ***
[n921:01432] Signal: Segmentation fault (11)
[n921:01432] Signal code: Address not mapped (1)
[n921:01432] Failing at address: 0xfffe10af11c0
[n921:01432] [ 0] [0x100428]
[n921:01432] [ 1] [0xfcc01f4]
[n921:01432] [ 2]
/home/rdiv1001/gromacs-4.5.3-linux_gcc445_fftw322/bin/mdrun_4.5.3_gcc_mpi(gmx_pme_do-0x51df30)
[0x1010c0e8]
[n921:01432] [ 3]
/home/rdiv1001/gromacs-4.5.3-linux_gcc445_fftw322/bin/mdrun_4.5.3_gcc_mpi(do_force_lowlevel-0x560cd0)
[0x100c88c8]
[n921:01432] [ 4]
/home/rdiv1001/gromacs-4.5.3-linux_gcc445_fftw322/bin/mdrun_4.5.3_gcc_mpi(do_force-0x50b084)
[0x1011f594]
[n921:01432] [ 5]
/home/rdiv1001/gromacs-4.5.3-linux_gcc445_fftw322/bin/mdrun_4.5.3_gcc_mpi(do_md-0x5bbb78)
[0x1006cac0]
[n921:01432] [ 6]
/home/rdiv1001/gromacs-4.5.3-linux_gcc445_fftw322/bin/mdrun_4.5.3_gcc_mpi(mdrunner-0x5c26f8)
[0x10065e98]
[n921:01432] [ 7]
/home/rdiv1001/gromacs-4.5.3-linux_gcc445_fftw322/bin/mdrun_4.5.3_gcc_mpi(main-0x5b7964)
[0x10070cec]
[n921:01432] [ 8] /lib64/libc.so.6 [0x80aaed8858]
[n921:01432] [ 9] /lib64/libc.so.6(__libc_start_main-0x1471f8) [0x80aaed8ad0]
[n921:01432] *** End of error message ***
I have not yet compiled with debugging enabled, but I can if that will be
useful.
-Justin
Justin A. Lemkul wrote:
Hi All,
I believe I have a resolution to all of this. It comes down to
compilers and FFTW. I had always used the same compilers to build all
my Gromacs versions (gcc-4.2.2 on Linux, gcc-3.3 on OSX) with the same
version of FFTW (3.0.1), primarily for reasons of continuity. Bug 715
that I posted before was due to a problem with FFTW, not Gromacs;
upgrading to 3.2.2 solves the issue. As well, the combination of
gcc-4.4.5 + FFTW 3.2.2 allows for successful free energy runs in my
tests thus far on Linux. Dependency issues on the OS X partition
prevent me from doing any upgrades, so we're out of luck there,
unfortunately. I will report back if any other weird behavior results,
but I believe the problem is solved.
I am no compiler/library guru, but it would seem to me that we've
reached a point where certain minimum versions must be required for
certain prerequisites. I would suggest that prior to the next release,
we come up with a list of what should be considered stable minimum
requirements (compiler versions, FFTW, anything else) to post on the
website and perhaps the manual. As it stands now, the prerequisites for
installation would seem to be satisfied by any C compiler and any
version of FFTW. Gromacs happily compiles under most conditions, but
shows some weird behavior if one is not using optimal dependencies.
Thanks to all for their input!
-Justin
Justin A. Lemkul wrote:
Michael Shirts wrote:
Hi, all-
Have you tried running
constraints = hbonds?
That might eliminate some of the constraint issues. Much less likely
for LINCS to break or have DD issues if only the hbonds are
constrained. 2 fs is not that big a deal for the heteroatom bonds.
I haven't yet, but I'll add it to my to-do list. I was
Re: [gmx-users] terminated but not completely
-cpi state.cpt -append try to add those two options at the end of your mdrun lina On Sun, Mar 13, 2011 at 5:53 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I run a simulation for 4 days. Unfortunately it terminated,but not completely,1 steps from 2 has done. Is there any way to run the continue of my files? Thanks in advance for your guidances Best Regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
