Re: [gmx-users] Normal Mode Analysis -- Expected Output
My problem was here: >nsteps = 10 which should read nsteps = 1 I was under the assumption that the step numbers would correspond to the number of calculated eigenvectors. All eigenvectors are calculated in step 1. Thanks, Bryan On Thu, Apr 11, 2013 at 12:33 PM, David van der Spoel wrote: > On 2013-04-11 17:57, Bryan Roessler wrote: > >> Hello, >> >> I am running a normal mode analysis on a ~1500AA protein with the >> following >> mdp parameters: >> >> Log file opened on Tue Apr 9 09:55:00 2013 >> Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 >> Gromacs version:VERSION 4.6.1 >> Precision: double >> Memory model: 64 bit >> MPI library:MPI >> OpenMP support: disabled >> GPU support:disabled >> invsqrt routine:gmx_software_invsqrt(x) >> CPU acceleration: AVX_256 >> FFT library:fftw-3.3.2-sse2 >> Large file support: enabled >> RDTSCP usage: enabled >> Built on: Fri Mar 15 09:20:59 CDT 2013 >> Built by: asndcy@uv [CMAKE] >> Build OS/arch: Linux 3.0.58-0.6.6-default x86_64 >> Build CPU vendor: GenuineIntel >> Build CPU brand:Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz >> Build CPU family: 6 Model: 45 Stepping: 7 >> Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr >> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 >> sse4.2 ssse3 tdt x2apic >> C compiler: /opt/sgi/mpt/mpt-2.07/bin/**mpicc GNU gcc (GCC) 4.7.2 >> C compiler flags: -mavx -Wextra -Wno-missing-field-**initializers >> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas >> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 >> -DNDEBUG >> >> >> :-) G R O M A C S (-: >> >> Good gRace! Old Maple Actually Chews Slate >> >> :-) VERSION 4.6.1 (-: >> >> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, >> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, >> >> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph >> Junghans, >> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, >> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, >> Michael Shirts, Alfons Sijbers, Peter Tieleman, >> >> Berk Hess, David van der Spoel, and Erik Lindahl. >> >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2012,2013, The GROMACS development team at >> Uppsala University & The Royal Institute of Technology, Sweden. >> check out http://www.gromacs.org for more information. >> >> This program is free software; you can redistribute it and/or >> modify it under the terms of the GNU Lesser General Public License >> as published by the Free Software Foundation; either version 2.1 >> of the License, or (at your option) any later version. >> >> :-) /opt/asn/apps/gromacs_4.6.1/**bin/mdrun_mpi_d (double >> precision) (-: >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl >> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable >> molecular simulation >> J. Chem. Theory Comput. 4 (2008) pp. 435-447 >> --- Thank You --- >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. >> C. >> Berendsen >> GROMACS: Fast, Flexible and Free >> J. Comp. Chem. 26 (2005) pp. 1701-1719 >> --- Thank You --- >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> E. Lindahl and B. Hess and D. van der Spoel >> GROMACS 3.0: A package for molecular simulation and trajectory analysis >> J. Mol. Mod. 7 (2001) pp. 306-317 >> --- Thank You --- >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> H. J. C. Berendsen, D. van der Spoel and R. van Drunen >> GROMACS: A message-passing parallel molecular dynamics implementation >> Comp. Phys. Comm. 91 (1995) pp. 43-56 >> --- Thank You --- >> >> >> Changing rlist from 1.47 to 1.4 for non-bonded 4x4 atom kernels >> >> Input Parameters: >> integrator = nm >> nsteps = 10 >> init-step= 0 >> cutoff-scheme= Verlet >> ns_type = Grid >> nstlist = 10 >> ndelta = 2 >> nstcomm = 100 >> comm-mode= Linear >> nstlog = 1000 >> nstxout = 500 >> nstvout = 500 >> nstfout = 500 >> nstcalcenergy= 100 >> nstenergy= 500 >> nstxtcout= 0 >> init-t
Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs
Hi Berk and others, Sorry it has been a long time since this issue was posted, but I got side-tracked from this issue with other projects. And I want to make sure I understand this correctly before venturing into more simulations. So this gets a little long winded, but I hope you will help me figure this out. So following up on the last emails perhaps the nomenclature is not consistent among the programs - which I shoudn't expect it to be either, so that is okay. I know this is the GMX list, but for clarity I will just describe what NAMD does, because it relates to how to run lipids in GMX (particularly with the GPU). NAMD: * When the switching function is on: "a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance". * A new "vdwForceSwitching" method is available as of version 2.7 - which applies a force-based switching function to the VDW term - similar I guess to how CHARMM does it. GMX: * The switch nomenclature is similar/identical to that in NAMD, in that the potential "energy" is switched off. * The "shift" method in Gromacs is equivalent to the "vdwForceSwitching" method in NAMD. And from what Berk was saying earlier and I heard this from Prof. Lindahl during the GPU webinar the other day too, the "shift" method is the only appropriate option and switching should not be used. It seems that this option is the one used for lipids in NAMD and CHARMM also, so that is great. Now regarding the GPU's you have to run with Verlet groups and here is where it get confusing because looking at the comparison table on the website "http://www.gromacs.org/Documentation/Cut-off_schemes"; ( I've extracted the important features of this table below). The switched interactions are not available using the Verlet groups and that is okay since that shouldn't be used anyways. But, the shifted interactions are "available", but only for the "energy" - now did we not just agree that when it is the energy that it should be called a "switched interaction"? Am I missing something here? Non-bonded interaction feature group Verlet exact cut-off shift/switch X cut-off X X shifted interactionsforce+energyenergy switched interactions X When I asked Prof. Lindahl during the excellent GPU webinar the other day, he said that switching was implemented and that is sort of what this table says too, but when we try to run a simulation using either switch or shift on the GPU we get the following error: "With Verlet lists only cut-off LJ interactions are supported" Now I can switch to an exact cut-off method at the cost of making the potential abruptly change to zero at the cut-off - minimizing the abruptness can be achieved by extending the cut-off, but then for the lipids CHARMM, MARTINI, and others, the cut-off seems to be an integral part of the force field development and changing it could prove problematic. So this leaves me to think that lipids simulations shouldn't be run on the GPU as it is currently, at least not without extensive testing. I'd appreciate any comments to all this rambling that can help clarify this for me... Thanks, Jesper On Jan 25, 2013, at 12:29 AM, Berk Hess wrote: > > Hi, > > The nomenclature is confusing here. > I don't recall the details of the switching in CHARMM. > But switch in Gromacs refers to switching the potential. > Shift in Gromacs refers to switching the force and thereby shifting the > potential. > > A switch on the force only (thus "shift" in Gromacs) can usually be matched > pretty > well by a plain cut-off with shifted potential by choosing the cut-off such > that either > the LJ potential matches the potential over the non-switched area or the > total LJ potential > energy matches for the system of interest. I expect these two cut-offs to be > very similar. > > Cheers, > > Berk > > >> Subject: Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs >> From: jesoren...@ucsd.edu >> Date: Thu, 24 Jan 2013 14:20:09 -0800 >> To: gmx-users@gromacs.org >> >> Hi Berk, >> >> I am running membrane simulations using both the CHARMM36 and MARTINI v. 2.1 >> parameters. >> So both those cut-off treatments are important to me, but if there are ways >> around it I'd be happy to explore them to be able to use the GPUs. The place >> it would be most effective would probably be for the all-atom simulations, >> as the number of particles is much higher in general, so switching would be >> the most important at this stage. >> >> On a similar note the switching done in gromacs is by the energy - correct? >> This has been mentioned as an issue for the CHARMM36 lipid parameters as it >> is the forces that are "normally" switche
Re: [gmx-users] Re: thermal conductivity,specific heat,enthalpy
On 2013-04-11 22:20, Ahmet yıldırım wrote: could anybody help me please? Check http://pubs.acs.org/doi/abs/10.1021/ct200731v 2013/4/11 Ahmet yıldırım Dear users, I calculated diffusion constant of a substance using g_msd tool. I also want to calculate thermal conductivity its. By the way,I did npt simulation. Diffusion constant=alpha Thermal conductivity=k specific heat=Cp density=d alpha=k/(d.Cp) and k=alpha.d.Cp I need d and Cp to calculate k. 1.) To calculate Cp: Prof. Spoel:From http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html cP = ( - ^2)/kB T^2 (NPT sim) The .edr file gives average enthalpy . According to above formula, I need both H and . How can I get H (not average)? 2.) .edr file: 1 LJ-(SR) 2 LJ-(LR) 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pressure10 Box-X 11 Box-Y 12 Box-Z 13 Volume 14 Density 15 pV 16 Enthalpy 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 Mu-X 37 Mu-Y38 Mu-Z39 T-System40 Lamb-System Firstly I calculated Entalphy (16) Afterward I calculated both Etot (7) and pV (15) Enthalpy=Etot+pV Unfortunately, I get "Enthalpy isnt equals to Etot+pV". Why? -- Ahmet Yıldırım -- 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] Simulation of the HEM-containing proteins
also I found such parameters in the native charm format (.prm) could you provide me with some script for conversion of tpr to itp? I could do such topology for cytochrome and add it to the contribution :) James 2013/4/12 James Starlight > I forgot to point out that when I made topology for cytochrome-HEME > complex ( assuming one cysteine covalently bonded to the FE ) again I've > forced with the lack of charmm parameters for such cysteine-HEME > interactions ( I've only found it for His coordinating bond). > > ERROR 1 [file topol.top, line 12409]: > No default Bond types > > > ERROR 2 [file topol.top, line 40454]: > No default U-B types > > > ERROR 3 [file topol.top, line 42130]: > No default U-B types > > > ERROR 4 [file topol.top, line 42131]: > No default U-B types > > > ERROR 5 [file topol.top, line 42132]: > No default U-B types > > > ERROR 6 [file topol.top, line 42133]: > No default U-B types > > > ERROR 7 [file topol.top, line 56994]: > > No default Proper Dih. types > > > ERROR 8 [file topol.top, line 56995]: > > No default Proper Dih. types > > > ERROR 9 [file topol.top, line 56996]: > > No default Proper Dih. types > > > ERROR 10 [file topol.top, line 56997]: > > No default Proper Dih. types > > > ERROR 11 [file topol.top, line 56998]: > > No default Proper Dih. types > > > ERROR 12 [file topol.top, line 56999]: > > No default Proper Dih. types > > > ERROR 13 [file topol.top, line 57000]: > > No default Proper Dih. types > > Also I've looked the literature for such parameters suitable for charm but > didnt find anything. > Does anybody here tried to simulate cytochrome ? > > > James > > > 2013/4/12 James Starlight > >> by the way also I've tried to make model of cytochrome p450 in charmm. In >> that case heme have only one coordinate bond with the side chain of >> cysteine (not 2 covalent bonds with cysteines as in the cytochrome-C). So >> as I understand I should include model of heme as the diffusion ligand ( as >> the separate itp file in the topology) should'n it ? >> How I can define coordinate bond of the heme's FE atom with the cysteine >> side chain (in the pdb2gmx I found that such can be done only for >> histidines)? >> >> James >> >> 2013/4/12 Mark Abraham >> >>> Look in the literature... >>> >>> >>> On Thu, Apr 11, 2013 at 2:12 PM, James Starlight >> >wrote: >>> >>> > During the past few days I've tried to make parametrization of any >>> > heme-containing cythochromes and always failed with the huge errors >>> about >>> > missing parameters. Could someone provide me with such params (i >>> suppose it >>> > should be added to thebonded/non-bonded.itps of the force field >>> besides the >>> > rtps) for any ful-atomic force field? Finally I've not found in mailing >>> > list any possible sollution of the same problems. >>> > >>> > >>> > James >>> > >>> > 2013/4/4 James Starlight >>> > >>> > > It was strange for me the big number of such errors :) >>> > > May the construction of new scheme for the hydrogens in the .hdb >>> file >>> > > partly solve my problem ? ( as I've mentioned previously i had >>> mismatch >>> > in >>> > > 2 hydrogens ( in comparison to the NMR-like structure). >>> > > Should also HEME be added in the residuetype.dat as the part of the >>> > > protein? >>> > > >>> > > Finally I'll be thankful to everyone who could provide me with the >>> any >>> > > cytochrome properly parametrized in charmm :) >>> > > >>> > > James >>> > > >>> > > >>> > > 2013/4/3 Justin Lemkul >>> > > >>> > >> On Wed, Apr 3, 2013 at 10:27 AM, James Starlight < >>> > jmsstarli...@gmail.com >>> > >> >wrote: >>> > >> >>> > >> > I've successfully parametrize cytochrome-HEME complex by means >>> pdb2gmx >>> > >> but >>> > >> > after processing that structure to grompp I've obtained errors >>> like >>> > >> > >>> > >> > ERROR 1 [file topol.top, line 2106]: >>> > >> > No default Bond types >>> > >> > >>> > >> > >>> > >> > ERROR 2 [file topol.top, line 2144]: >>> > >> > No default Bond types >>> > >> > >>> > >> > >>> > >> > ERROR 3 [file topol.top, line 3153]: >>> > >> > No default Bond types >>> > >> > >>> > >> > >>> > >> > ERROR 4 [file topol.top, line 8725]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 5 [file topol.top, line 8792]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 6 [file topol.top, line 10624]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 7 [file topol.top, line 10625]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 8 [file topol.top, line 11382]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 9 [file topol.top, line 11383]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 10 [file topol.top, line 11384]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 11 [file topol.top, line 11385]: >>> > >> > No default U-B types >>> > >> > >>> > >> > >>> > >> > ERROR 12 [file
Re: [gmx-users] Re: cygwin_mpi_gmx installation
On Fri, Apr 12, 2013 at 3:45 PM, 라지브간디 wrote: > Thanks for your answers. I have uninstalled the mpi, have also reinstalled > the CUDA and got the same issue. As you have mentioned before I noticed that > it struggle to detect the CUDA. Do you mean that you reconfigured without MPI and with CUDA? You don't need to uninstall anything to enable/disable configuration options, just clean your build directory and rerun CMake in it. > > > Can cygwin recognize the CUDA installed in win 7? if so, how do i link them ? Good question, I've no idea whether it can as I myself have never built GROMACS with CUDA on cygwin neither have I heard of anyone else do that. What I can safely state is that the native Win builds with non-cygwin CMake and MSVC as a compiler do work with with a variety of generators: nmake, ninja, and VS. However, it would be very useful to know whether/how it is possible to detect CUDA with CMake a build GROMACS with GPU acceleration on cygwin. Perhaps someone else on the list with more cygwin experience could help out with tips or even try to build with CUDA. > > > The default installation path of CUDA in win 7 could be C:\Program > Files\NVIDIA GPU Computing Toolkit\CUDA > > > If I am correct, it should be like > > > cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=C:\Program Files\NVIDIA GPU > Computing Toolkit\CUDA The whitespaces will need special treatment, AFAIR putting quotes around the path (or simply copying the directory to C:\CUDA) should work. Alternatively, you could try to put nvcc in your path, than CMake should be able to do the path handling magic. > > > Kindly give me your suggestion. Thanks in advance. > > > Subject: Re: [gmx-users] cygwin_mpi_gmx installation > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > Indeed it's strange. In fact, it seems that CUDA detection did not > even run, there should be a message whether it found the toolkit or > not just before the "Enabling native GPU acceleration" - and the > enabling should not even happen without CUDA detected. > > Unrelated, but do you really need MPI with cygwin? Unless you are > planning to run on multiple Windows machines, the default thread-MPI > parallelization is enough to use multiple cores! > > Cheers, > -- > Szil��rd > > > On Fri, Apr 12, 2013 at 1:04 PM, Mark Abraham > wrote: >> That looks really strange. CMake claims to detect CUDA but the right >> variables are not set. >> >> 1) Can you reproduce this in a clean build directory? >> 2) If so, what CUDA is present? >> >> Mark > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] install gromacs 4.6.1 on 64bit Windows 7 cygwin
On Fri, Apr 12, 2013 at 5:53 PM, Hua Lu wrote: > Hi! > I got the following error message while compiling gromacs using a complete > installation of Cygwin on 64bit windows 7. Any idea what the problem is? > Yes, you can't read those files. We can't know why. You wrote them as a different user, or with different permissions, or something. Mark This is what I have used to install as detailed on the gromacs website: > > cd gromacs-4.6.1 > mkdir build > cd build, cmake .. -DGMX_BUILD_OWN_FFTW=ON > make > > the error occur at the last step 'make' > > > Thanks, Hua > > .. > Scanning dependencies of target gmx > [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o > /cygdrive/d/gromacs-4.6.1/src/gmxlib/3dview.c:39:20: fatal error: > /cygdrive/d/gromacs-4.6.1/build/src/config.h: Permission denied > compilation terminated. > src/gmxlib/CMakeFiles/gmx.dir/build.make:57: recipe for target > `src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o' failed > make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o] Error 1 > CMakeFiles/Makefile2:1238: recipe for target > `src/gmxlib/CMakeFiles/gmx.dir/all' failed > make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 > Makefile:146: recipe for target `all' failed > make: *** [all] Error 2 > > > > University of Greenwich, a charity and company limited by guarantee, > registered in England (reg. no. 986729). Registered office: > Old Royal Naval College, Park Row, Greenwich, London SE10 9LS. > -- > 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] Dihedral angle PCA
On Fri, 12 Apr 2013, Thomas Evangelidis wrote: On 12 April 2013 07:51, anu chandra wrote: Hi David, Thanks for the reply. I have not tried yet. Since I didn’t find query about the dihedral PCA in the mail list, I thought of confirm about the steps mentioned in the web site. Regarding the use of dihedral PCA, the protein with which I am working behave differently from others. From literature, this protein shows minimal backbone conformational changes during ligand binding and presumed that there is high degree of side-chain conformational changes during binding to ligand. This made me to think about dihedral PCA for get some information about the ligand binding. What is your opinion in this regard? Why not Cartesian PCA restricted to the protein backbone ? dPCA is preferred in cases of peptides or intrinsically disordered proteins. Even for very flexible systems, I would say that your choice between dPCA and cPCA should depend on what you want, since your similarity metric should match as close as possible the property you want to measure. Since the underlying conformational spaces of dPCA and cPCA are generally quite distorted relative to each other, they can give quite different distances between conformations. For example, you can have two conformers that look very different in 3D space due to a series of very small cumulative dihedral differences, meaning that they are very distant in cPCA space but very close in dPCA space. Conversely, you can have two conformers that look very similar in 3D space due to a few very different dihedrals which compensate each other, meaning that they are very close in cPCA space but very distant in dPCA space. So, if you want to do a detailed analysis of conformational kinetics, dPCA is probably a good choice, because it better retains the kinetic contiguity of torsional states. But if you are interested in molecular recognition (ligand-receptor interactions, etc), you should probably choose cPCA, because it better maps the overall 3D shape (assuming you can devise a good reference structure for fit). Anyway, you have to think about your problem and decide what better suits it. You can see some examples and a discussion of these issues (including using other metrics) in http://dx.doi.org/10.1021/jp902991u. There is a very simple test you can do (check the paper): take all pairs of simulated conformations and compute their distance in dPCA space and in cPCA space (using all dimensions, not just the selected PCs), and then make a scatter plot of one against the other. If the two distances are poorly correlated, dPCA and cPCA can give quite different results. Best, Antonio Is there any other sort of analyses that can help me to quantify such side-chain conformational changes and also to locate the regions in protein, which have high degree of side-chain conformational changes during ligand binding? Waiting for your valuable reply. Thanks and regards Anu -- 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 -- Antonio M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN, 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista -- -- 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] install gromacs 4.6.1 on 64bit Windows 7 cygwin
Hi! I got the following error message while compiling gromacs using a complete installation of Cygwin on 64bit windows 7. Any idea what the problem is? This is what I have used to install as detailed on the gromacs website: cd gromacs-4.6.1 mkdir build cd build, cmake .. -DGMX_BUILD_OWN_FFTW=ON make the error occur at the last step 'make' Thanks, Hua .. Scanning dependencies of target gmx [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o /cygdrive/d/gromacs-4.6.1/src/gmxlib/3dview.c:39:20: fatal error: /cygdrive/d/gromacs-4.6.1/build/src/config.h: Permission denied compilation terminated. src/gmxlib/CMakeFiles/gmx.dir/build.make:57: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o' failed make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o] Error 1 CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 University of Greenwich, a charity and company limited by guarantee, registered in England (reg. no. 986729). Registered office: Old Royal Naval College, Park Row, Greenwich, London SE10 9LS. -- 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: cygwin_mpi_gmx installation
Thanks for your answers. I have uninstalled the mpi, have also reinstalled the CUDA and got the same issue. As you have mentioned before I noticed that it struggle to detect the CUDA. Can cygwin recognize the CUDA installed in win 7? if so, how do i link them ? The default installation path of CUDA in win 7 could be C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA If I am correct, it should be like cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA Kindly give me your suggestion. Thanks in advance. Subject: Re: [gmx-users] cygwin_mpi_gmx installation To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=UTF-8 Indeed it's strange. In fact, it seems that CUDA detection did not even run, there should be a message whether it found the toolkit or not just before the "Enabling native GPU acceleration" - and the enabling should not even happen without CUDA detected. Unrelated, but do you really need MPI with cygwin? Unless you are planning to run on multiple Windows machines, the default thread-MPI parallelization is enough to use multiple cores! Cheers, -- Szil��rd On Fri, Apr 12, 2013 at 1:04 PM, Mark Abraham wrote: > That looks really strange. CMake claims to detect CUDA but the right > variables are not set. > > 1) Can you reproduce this in a clean build directory? > 2) If so, what CUDA is present? > > Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] lysine side chain shrinking
Dear All, During a simulation of a protein with a ligand, I see the -NH3 of the lysine side chain near the ligand is getting squeezed for a very short time; N-H bonds are getting contracted and the angle are no longer within tetrahedral normal http://lists.gromacs.org/pipermail/gmx-users/2010-November/056094.html] in the mailing list but found little helpful. For my case the simulation does not give me any warning. Please suggest me if there is any problem with my simulation protocol. The '.mdp' file is given as follows integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode =linear ; 7.3.8 Output Control nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 2000 nstenergy = 2000 nstxtcout = 2000 xtc_precision = 2000 xtc_grps= System energygrps = System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.4 ; 7.3.11 VdW vdwtype = cut-off rvdw= 1.4 DispCorr= EnerPres ; 7.3.13 Ewald fourierspacing = 0.14 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = system tau_t = 1.0 ref_t = 300 ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 113969 ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm= LINCS continuation= yes lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Thanks, Tarak -- 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] Fwd: [Fwd: QM MM modification]
Hi Natalia, I am not aware whether the QM/MM implementation in GROMACS works in 4.6, nor with which Gaussian version was intended to work in the past. Perhaps Gerrit Groenhof or someone on gmx-users can update us here? I'm not sure what "diff file" you are seeking, either. Can you elaborate please? Mark -- Forwarded message -- From: Date: Fri, Apr 12, 2013 at 1:53 PM Subject: [Fwd: QM MM modification] To: mark.abra...@scilifelab.se Good afternoon! My name is Natallia Kulik and I am working in Czech Academy of Sciences on the project of simulation oh substrate-enzyme interaction of hexosaminidases. I want to use Gromacs 4.6 with QM implementation (Gaussian 09) for my calculation. However unfortunately we can't correctly change gaussian file. Could you, please, send us diff-file from the original version of gaussian (for gaussian 09 or 03)? Thank you very much, Natallia -- 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] pbc problem
On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen wrote:
> Dear All,
>
> I made a POPC bilayer and carried out embedding a protein into this
> membrane. But the fatal error has appeared :
> Fatal error:
> Something is wrong with your membrane. Max and min z values are 12.342000
> and 0.016000. Maybe your membrane is not centered in the box, but located
> at the box edge in the z-direction, so that one membrane is distributed
> over two periodic box images. Another possibility is that your water layer
> is not thick enough.
>
> I think my bilayer stay at between two periodic images. What should i do to
> put it in corrected position ?
>
>
It should be a very simple matter of visualization. Use editconf -center to
place the membrane wherever you want within the unit cell. You can remove
the uncertainty ("I think" is weak compared to "I know") by looking at the
box vectors and then numerically determining the center of the membrane
with g_traj. That should provide you with all the information you need to
determine what's going on.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Simulation of the HEM-containing proteins
I forgot to point out that when I made topology for cytochrome-HEME complex ( assuming one cysteine covalently bonded to the FE ) again I've forced with the lack of charmm parameters for such cysteine-HEME interactions ( I've only found it for His coordinating bond). ERROR 1 [file topol.top, line 12409]: No default Bond types ERROR 2 [file topol.top, line 40454]: No default U-B types ERROR 3 [file topol.top, line 42130]: No default U-B types ERROR 4 [file topol.top, line 42131]: No default U-B types ERROR 5 [file topol.top, line 42132]: No default U-B types ERROR 6 [file topol.top, line 42133]: No default U-B types ERROR 7 [file topol.top, line 56994]: No default Proper Dih. types ERROR 8 [file topol.top, line 56995]: No default Proper Dih. types ERROR 9 [file topol.top, line 56996]: No default Proper Dih. types ERROR 10 [file topol.top, line 56997]: No default Proper Dih. types ERROR 11 [file topol.top, line 56998]: No default Proper Dih. types ERROR 12 [file topol.top, line 56999]: No default Proper Dih. types ERROR 13 [file topol.top, line 57000]: No default Proper Dih. types Also I've looked the literature for such parameters suitable for charm but didnt find anything. Does anybody here tried to simulate cytochrome ? James 2013/4/12 James Starlight > by the way also I've tried to make model of cytochrome p450 in charmm. In > that case heme have only one coordinate bond with the side chain of > cysteine (not 2 covalent bonds with cysteines as in the cytochrome-C). So > as I understand I should include model of heme as the diffusion ligand ( as > the separate itp file in the topology) should'n it ? > How I can define coordinate bond of the heme's FE atom with the cysteine > side chain (in the pdb2gmx I found that such can be done only for > histidines)? > > James > > 2013/4/12 Mark Abraham > >> Look in the literature... >> >> >> On Thu, Apr 11, 2013 at 2:12 PM, James Starlight > >wrote: >> >> > During the past few days I've tried to make parametrization of any >> > heme-containing cythochromes and always failed with the huge errors >> about >> > missing parameters. Could someone provide me with such params (i >> suppose it >> > should be added to thebonded/non-bonded.itps of the force field besides >> the >> > rtps) for any ful-atomic force field? Finally I've not found in mailing >> > list any possible sollution of the same problems. >> > >> > >> > James >> > >> > 2013/4/4 James Starlight >> > >> > > It was strange for me the big number of such errors :) >> > > May the construction of new scheme for the hydrogens in the .hdb file >> > > partly solve my problem ? ( as I've mentioned previously i had >> mismatch >> > in >> > > 2 hydrogens ( in comparison to the NMR-like structure). >> > > Should also HEME be added in the residuetype.dat as the part of the >> > > protein? >> > > >> > > Finally I'll be thankful to everyone who could provide me with the any >> > > cytochrome properly parametrized in charmm :) >> > > >> > > James >> > > >> > > >> > > 2013/4/3 Justin Lemkul >> > > >> > >> On Wed, Apr 3, 2013 at 10:27 AM, James Starlight < >> > jmsstarli...@gmail.com >> > >> >wrote: >> > >> >> > >> > I've successfully parametrize cytochrome-HEME complex by means >> pdb2gmx >> > >> but >> > >> > after processing that structure to grompp I've obtained errors like >> > >> > >> > >> > ERROR 1 [file topol.top, line 2106]: >> > >> > No default Bond types >> > >> > >> > >> > >> > >> > ERROR 2 [file topol.top, line 2144]: >> > >> > No default Bond types >> > >> > >> > >> > >> > >> > ERROR 3 [file topol.top, line 3153]: >> > >> > No default Bond types >> > >> > >> > >> > >> > >> > ERROR 4 [file topol.top, line 8725]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 5 [file topol.top, line 8792]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 6 [file topol.top, line 10624]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 7 [file topol.top, line 10625]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 8 [file topol.top, line 11382]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 9 [file topol.top, line 11383]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 10 [file topol.top, line 11384]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 11 [file topol.top, line 11385]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 12 [file topol.top, line 11491]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 13 [file topol.top, line 11492]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 14 [file topol.top, line 11493]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 15 [file topol.top, line 11506]: >> > >> > No default U-B types >> > >> > >> > >> > >> > >> > ERROR 16 [file topol.top, line 11507]: >> > >> > No default U-B types >> > >> >
[gmx-users] pbc problem
Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and 0.016000. Maybe your membrane is not centered in the box, but located at the box edge in the z-direction, so that one membrane is distributed over two periodic box images. Another possibility is that your water layer is not thick enough. I think my bilayer stay at between two periodic images. What should i do to put it in corrected position ? Thankful for any help ! Regards, Thu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dihedral angle PCA
> > > dPCA is > > preferred in cases of peptides or intrinsically disordered proteins. > > > > And even then a disordered mess can still be a disordered mess... > > Very true! -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dihedral angle PCA
On Fri, Apr 12, 2013 at 11:28 AM, Thomas Evangelidis wrote: > On 12 April 2013 07:51, anu chandra wrote: > > > Hi David, > > > > Thanks for the reply. I have not tried yet. Since I didn’t find query > about > > the dihedral PCA in the mail list, I thought of confirm about the steps > > mentioned in the web site. > > > > > > Regarding the use of dihedral PCA, the protein with which I am working > > behave differently from others. From literature, this protein shows > minimal > > backbone conformational changes during ligand binding and presumed that > > there is high degree of side-chain conformational changes during binding > to > > ligand. This made me to think about dihedral PCA for get some information > > about the ligand binding. What is your opinion in this regard? > > > > > Why not Cartesian PCA restricted to the protein backbone ? Ja. Fit to the backbone, and measure on the side chains. In principle, any kind of difference metric could work. RMSD of side chain atoms vs backbone atoms is all you need for "are the side chains the ones changing upon binding?" > dPCA is > preferred in cases of peptides or intrinsically disordered proteins. > And even then a disordered mess can still be a disordered mess... Mark > > Is there any other sort of analyses that can help me to quantify such > > side-chain conformational changes and also to locate the regions in > > protein, which have high degree of side-chain conformational changes > > during ligand binding? > > > > Waiting for your valuable reply. > > > > Thanks and regards > > Anu > > > > > > > -- > 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] cygwin_mpi_gmx installation
Indeed it's strange. In fact, it seems that CUDA detection did not even run, there should be a message whether it found the toolkit or not just before the "Enabling native GPU acceleration" - and the enabling should not even happen without CUDA detected. Unrelated, but do you really need MPI with cygwin? Unless you are planning to run on multiple Windows machines, the default thread-MPI parallelization is enough to use multiple cores! Cheers, -- Szilárd On Fri, Apr 12, 2013 at 1:04 PM, Mark Abraham wrote: > That looks really strange. CMake claims to detect CUDA but the right > variables are not set. > > 1) Can you reproduce this in a clean build directory? > 2) If so, what CUDA is present? > > Mark > > > On Thu, Apr 11, 2013 at 2:57 PM, 라지브간디 wrote: > >> Dear gmx, >> >> >> I have installed mpich for MPI use in cygwin (Win 7 -64 bit) and >> encountered the following error : I dont understand what I am missing here? >> >> >> $ cmake .. -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON >> >> >> -- The C compiler identification is GNU 4.8.0 >> -- Check for working C compiler: /usr/bin/gcc.exe >> -- Check for working C compiler: /usr/bin/gcc.exe -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Looking for NVIDIA GPUs present in the system >> -- Could not detect NVIDIA GPUs >> -- Enabling native GPU acceleration >> -- The CXX compiler identification is GNU 4.8.0 >> -- Check for working CXX compiler: /usr/bin/c++.exe >> -- Check for working CXX compiler: /usr/bin/c++.exe -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> -- Checking for GCC x86 inline asm >> -- Checking for GCC x86 inline asm - supported >> -- Detecting best acceleration for this CPU >> -- Detecting best acceleration for this CPU - AVX_256 >> -- Try OpenMP C flag = [-fopenmp] >> -- Performing Test OpenMP_FLAG_DETECTED >> -- Performing Test OpenMP_FLAG_DETECTED - Success >> -- Try OpenMP CXX flag = [-fopenmp] >> -- Performing Test OpenMP_FLAG_DETECTED >> -- Performing Test OpenMP_FLAG_DETECTED - Success >> -- Found OpenMP: -fopenmp >> -- Performing Test CFLAGS_WARN >> -- Performing Test CFLAGS_WARN - Success >> -- Performing Test CFLAGS_WARN_EXTRA >> -- Performing Test CFLAGS_WARN_EXTRA - Success >> -- Performing Test CFLAGS_EXCESS_PREC >> -- Performing Test CFLAGS_EXCESS_PREC - Success >> -- Performing Test CFLAGS_COPT >> -- Performing Test CFLAGS_COPT - Success >> -- Performing Test CFLAGS_NOINLINE >> -- Performing Test CFLAGS_NOINLINE - Success >> -- Performing Test CXXFLAGS_WARN >> -- Performing Test CXXFLAGS_WARN - Success >> -- Performing Test CXXFLAGS_WARN_EXTRA >> -- Performing Test CXXFLAGS_WARN_EXTRA - Success >> -- Performing Test CXXFLAGS_EXCESS_PREC >> -- Performing Test CXXFLAGS_EXCESS_PREC - Success >> -- Performing Test CXXFLAGS_COPT >> -- Performing Test CXXFLAGS_COPT - Success >> -- Performing Test CXXFLAGS_NOINLINE >> -- Performing Test CXXFLAGS_NOINLINE - Success >> -- Using default binary suffix: "_mpi" >> -- Using default library suffix: "_mpi" >> -- Looking for include file string.h >> -- Looking for include file string.h - found >> -- Looking for include file math.h >> -- Looking for include file math.h - found >> -- Looking for include file limits.h >> -- Looking for include file limits.h - found >> -- Looking for include file memory.h >> -- Looking for include file memory.h - found >> -- Looking for include file unistd.h >> -- Looking for include file unistd.h - found >> -- Looking for include file direct.h >> -- Looking for include file direct.h - not found >> -- Looking for include file pwd.h >> -- Looking for include file pwd.h - found >> -- Looking for include file stdint.h >> -- Looking for include file stdint.h - found >> -- Looking for include file stdlib.h >> -- Looking for include file stdlib.h - found >> -- Looking for include file pthread.h >> -- Looking for include file pthread.h - found >> -- Looking for include file dirent.h >> -- Looking for include file dirent.h - found >> -- Looking for include file inttypes.h >> -- Looking for include file inttypes.h - found >> -- Looking for include file regex.h >> -- Looking for include file regex.h - found >> -- Looking for include file sys/types.h >> -- Looking for include file sys/types.h - found >> -- Looking for include file sys/stat.h >> -- Looking for include file sys/stat.h - found >> -- Looking for include file sys/time.h >> -- Looking for include file sys/time.h - found >> -- Looking for include file rpc/rpc.h >> -- Looking for include file rpc/rpc.h - not found >> -- Looking for include files rpc/rpc.h, rpc/xdr.h >> -- Looking for include files rpc/rpc.h, rpc/xdr.h - not found >> -- Looking for include file io.h >> -- Looking for include file io.h - found >> -- Looking for include file sched.h >> -- Looking for include file sched.h - found >> -- Looking for strcasecmp >> -- Looking for strcasecmp - found >> -- Looking for strdup >> -- Looking for strdup - found >> -- Looking fo
Re: [gmx-users] cygwin_mpi_gmx installation
That looks really strange. CMake claims to detect CUDA but the right variables are not set. 1) Can you reproduce this in a clean build directory? 2) If so, what CUDA is present? Mark On Thu, Apr 11, 2013 at 2:57 PM, 라지브간디 wrote: > Dear gmx, > > > I have installed mpich for MPI use in cygwin (Win 7 -64 bit) and > encountered the following error : I dont understand what I am missing here? > > > $ cmake .. -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON > > > -- The C compiler identification is GNU 4.8.0 > -- Check for working C compiler: /usr/bin/gcc.exe > -- Check for working C compiler: /usr/bin/gcc.exe -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Looking for NVIDIA GPUs present in the system > -- Could not detect NVIDIA GPUs > -- Enabling native GPU acceleration > -- The CXX compiler identification is GNU 4.8.0 > -- Check for working CXX compiler: /usr/bin/c++.exe > -- Check for working CXX compiler: /usr/bin/c++.exe -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Checking for GCC x86 inline asm > -- Checking for GCC x86 inline asm - supported > -- Detecting best acceleration for this CPU > -- Detecting best acceleration for this CPU - AVX_256 > -- Try OpenMP C flag = [-fopenmp] > -- Performing Test OpenMP_FLAG_DETECTED > -- Performing Test OpenMP_FLAG_DETECTED - Success > -- Try OpenMP CXX flag = [-fopenmp] > -- Performing Test OpenMP_FLAG_DETECTED > -- Performing Test OpenMP_FLAG_DETECTED - Success > -- Found OpenMP: -fopenmp > -- Performing Test CFLAGS_WARN > -- Performing Test CFLAGS_WARN - Success > -- Performing Test CFLAGS_WARN_EXTRA > -- Performing Test CFLAGS_WARN_EXTRA - Success > -- Performing Test CFLAGS_EXCESS_PREC > -- Performing Test CFLAGS_EXCESS_PREC - Success > -- Performing Test CFLAGS_COPT > -- Performing Test CFLAGS_COPT - Success > -- Performing Test CFLAGS_NOINLINE > -- Performing Test CFLAGS_NOINLINE - Success > -- Performing Test CXXFLAGS_WARN > -- Performing Test CXXFLAGS_WARN - Success > -- Performing Test CXXFLAGS_WARN_EXTRA > -- Performing Test CXXFLAGS_WARN_EXTRA - Success > -- Performing Test CXXFLAGS_EXCESS_PREC > -- Performing Test CXXFLAGS_EXCESS_PREC - Success > -- Performing Test CXXFLAGS_COPT > -- Performing Test CXXFLAGS_COPT - Success > -- Performing Test CXXFLAGS_NOINLINE > -- Performing Test CXXFLAGS_NOINLINE - Success > -- Using default binary suffix: "_mpi" > -- Using default library suffix: "_mpi" > -- Looking for include file string.h > -- Looking for include file string.h - found > -- Looking for include file math.h > -- Looking for include file math.h - found > -- Looking for include file limits.h > -- Looking for include file limits.h - found > -- Looking for include file memory.h > -- Looking for include file memory.h - found > -- Looking for include file unistd.h > -- Looking for include file unistd.h - found > -- Looking for include file direct.h > -- Looking for include file direct.h - not found > -- Looking for include file pwd.h > -- Looking for include file pwd.h - found > -- Looking for include file stdint.h > -- Looking for include file stdint.h - found > -- Looking for include file stdlib.h > -- Looking for include file stdlib.h - found > -- Looking for include file pthread.h > -- Looking for include file pthread.h - found > -- Looking for include file dirent.h > -- Looking for include file dirent.h - found > -- Looking for include file inttypes.h > -- Looking for include file inttypes.h - found > -- Looking for include file regex.h > -- Looking for include file regex.h - found > -- Looking for include file sys/types.h > -- Looking for include file sys/types.h - found > -- Looking for include file sys/stat.h > -- Looking for include file sys/stat.h - found > -- Looking for include file sys/time.h > -- Looking for include file sys/time.h - found > -- Looking for include file rpc/rpc.h > -- Looking for include file rpc/rpc.h - not found > -- Looking for include files rpc/rpc.h, rpc/xdr.h > -- Looking for include files rpc/rpc.h, rpc/xdr.h - not found > -- Looking for include file io.h > -- Looking for include file io.h - found > -- Looking for include file sched.h > -- Looking for include file sched.h - found > -- Looking for strcasecmp > -- Looking for strcasecmp - found > -- Looking for strdup > -- Looking for strdup - found > -- Looking for vprintf > -- Looking for vprintf - found > -- Looking for memcmp > -- Looking for memcmp - found > -- Looking for posix_memalign > -- Looking for posix_memalign - found > -- Looking for memalign > -- Looking for memalign - found > -- Looking for _aligned_malloc > -- Looking for _aligned_malloc - not found > -- Looking for gettimeofday > -- Looking for gettimeofday - found > -- Looking for isnan > -- Looking for isnan - found > -- Looking for _isnan > -- Looking for _isnan - not found > -- Looking for fsync > -- Looking for fsync - found > -- Looking for _fileno > -- Looking for _fileno - not found > -- Looking for fileno > -
[gmx-users] Re: Is it possible to pull 2 different groups with respect to a third group as reference?
Yes, from 4.5.x manual: pull_ngroups: (1) The number of pull groups, not including the reference group. [...] Just set 'pull_ngroups = 2' and then make entries for pull_group1 -> pull_vec1 ... pull_group2 -> pull_vec2 ... and so on... greetings thomas Am 12.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org: I have 3 groups on the system, and I want to pull 2 groups with respect to the 3rd one. Is it possible in GROMACS? Thanking you, Saikat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dihedral angle PCA
On 12 April 2013 07:51, anu chandra wrote: > Hi David, > > Thanks for the reply. I have not tried yet. Since I didn’t find query about > the dihedral PCA in the mail list, I thought of confirm about the steps > mentioned in the web site. > > > Regarding the use of dihedral PCA, the protein with which I am working > behave differently from others. From literature, this protein shows minimal > backbone conformational changes during ligand binding and presumed that > there is high degree of side-chain conformational changes during binding to > ligand. This made me to think about dihedral PCA for get some information > about the ligand binding. What is your opinion in this regard? > > Why not Cartesian PCA restricted to the protein backbone ? dPCA is preferred in cases of peptides or intrinsically disordered proteins. > Is there any other sort of analyses that can help me to quantify such > side-chain conformational changes and also to locate the regions in > protein, which have high degree of side-chain conformational changes > during ligand binding? > > Waiting for your valuable reply. > > Thanks and regards > Anu > > > -- 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] Simulation of the HEM-containing proteins
by the way also I've tried to make model of cytochrome p450 in charmm. In that case heme have only one coordinate bond with the side chain of cysteine (not 2 covalent bonds with cysteines as in the cytochrome-C). So as I understand I should include model of heme as the diffusion ligand ( as the separate itp file in the topology) should'n it ? How I can define coordinate bond of the heme's FE atom with the cysteine side chain (in the pdb2gmx I found that such can be done only for histidines)? James 2013/4/12 Mark Abraham > Look in the literature... > > > On Thu, Apr 11, 2013 at 2:12 PM, James Starlight >wrote: > > > During the past few days I've tried to make parametrization of any > > heme-containing cythochromes and always failed with the huge errors about > > missing parameters. Could someone provide me with such params (i suppose > it > > should be added to thebonded/non-bonded.itps of the force field besides > the > > rtps) for any ful-atomic force field? Finally I've not found in mailing > > list any possible sollution of the same problems. > > > > > > James > > > > 2013/4/4 James Starlight > > > > > It was strange for me the big number of such errors :) > > > May the construction of new scheme for the hydrogens in the .hdb file > > > partly solve my problem ? ( as I've mentioned previously i had mismatch > > in > > > 2 hydrogens ( in comparison to the NMR-like structure). > > > Should also HEME be added in the residuetype.dat as the part of the > > > protein? > > > > > > Finally I'll be thankful to everyone who could provide me with the any > > > cytochrome properly parametrized in charmm :) > > > > > > James > > > > > > > > > 2013/4/3 Justin Lemkul > > > > > >> On Wed, Apr 3, 2013 at 10:27 AM, James Starlight < > > jmsstarli...@gmail.com > > >> >wrote: > > >> > > >> > I've successfully parametrize cytochrome-HEME complex by means > pdb2gmx > > >> but > > >> > after processing that structure to grompp I've obtained errors like > > >> > > > >> > ERROR 1 [file topol.top, line 2106]: > > >> > No default Bond types > > >> > > > >> > > > >> > ERROR 2 [file topol.top, line 2144]: > > >> > No default Bond types > > >> > > > >> > > > >> > ERROR 3 [file topol.top, line 3153]: > > >> > No default Bond types > > >> > > > >> > > > >> > ERROR 4 [file topol.top, line 8725]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 5 [file topol.top, line 8792]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 6 [file topol.top, line 10624]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 7 [file topol.top, line 10625]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 8 [file topol.top, line 11382]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 9 [file topol.top, line 11383]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 10 [file topol.top, line 11384]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 11 [file topol.top, line 11385]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 12 [file topol.top, line 11491]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 13 [file topol.top, line 11492]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 14 [file topol.top, line 11493]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 15 [file topol.top, line 11506]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 16 [file topol.top, line 11507]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 17 [file topol.top, line 11508]: > > >> > No default U-B types > > >> > > > >> > > > >> > ERROR 18 [file topol.top, line 12147]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 19 [file topol.top, line 12148]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 20 [file topol.top, line 12149]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 21 [file topol.top, line 12150]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 22 [file topol.top, line 12151]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 23 [file topol.top, line 12152]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 24 [file topol.top, line 12247]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 25 [file topol.top, line 12248]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 26 [file topol.top, line 12249]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 27 [file topol.top, line 12250]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 28 [file topol.top, line 12251]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 29 [file topol.top, line 12252]: > > >> > No default Proper Dih. types > > >> > > > >> > > > >> > ERROR 30 [file topol.top, line 14948]: > > >> > No default Proper Dih. types
