[gmx-users] Topology of Graphite Oxide
Hi users: I want to run a simulation of adsorption of protein on graphite oxide(GO) which is oxidized at random and is near 80% coverage by hydroxyl and epoxyl group. My first question is how to generate a topology filefor GO. Previous to search solution to this problem in this forum, I had tried to make a topology for GO use g_x2top with command: g_x2top -f input.pdb -nopbc -r outputname -o outputname. But g_x2top did not work fine(fine for prestine graphite) and gave error messages like Can not find forcefield for atom .. My second also is about definition of improper dihedral in opls-aa. Whether it is validate to assign a improper dihedral for a central sp2 carbon atom with three other bonded atoms no matter of what is type of other three atom? I have gotten (mentioned above) a topology file of pristine graphite for opls-aa with g_x2top(the command is similar to above), but the topology file did not include any improper dihedral. I will appreciated you for giving any advice. sincerely zhhxu PhD student Institute of Process Engineering, Chinese Academy of Sciences, Department of Biochemical Engineering. -- 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
AW: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
Hi Nilesh, So far I have not been able to figure out the problem. I also ran some new simulations with Gromacs 4.6 for 100ps of EMIMDCA and everything worked fine. I looked into the code, but was not able to detect the problem that causes the strange behavior you are observing. Can you update your Gromacs version to 4.6.1 and try again? /Flo -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Mittwoch, 6. März 2013 17:19 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current Hello, I run a 500ps simulation and save the trajectory each 3fs. g_current work till 498ps and later it shows -nan. Can you tell where is the problem Nilesh Hi, Now I've tested the version of g_current in 4.6 and for me it works fine. /Flo -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Florian Dommert Gesendet: Mittwoch, 27. Februar 2013 18:46 An: 'Discussion list for GROMACS users' Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Mittwoch, 27. Februar 2013 17:38 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current Hello, I am using g_current for first time. Now I am running additional simulation and I will save trajectory at 2 fs. Is it possible to calculate contribution of rotational and translation to dipole moment simultaneously with the simulation instead of saving the trajectory at each 2fs? Hi, This is one of my majors on my to do list, but currently not possible. I think a saving frequency of 0.05 ps should be fine. /Flo Nilesh Hi, Have you done a similar analysis with another IL system or is it the first time you use g_current? Currently I am not able to figure out what the problem is. However 2ps saving interval is quite long for such a kind of analysis. A zero value of the translational dipole moment hints to neutral molecules which should not be the case for your system. What is written in the output of mj.xvg. Is filled with zeros? /Flo -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Mittwoch, 27. Februar 2013 15:26 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current Hello, Yes. Segfault is solved. I saving velocites and coordinates at 2 ps. Nilesh Hi, At least the segfault is solved. However, the zero output of M_J for your IL system is really strange. I'm thinking about a reason, but I am currently not able to find one. How often do you write out velocities and coordinates in your trr file? /Flo -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Dienstag, 26. Februar 2013 17:50 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current Hello, I didn't get any segmental fault if I use Gromacs Version 4.5.5. g_current -f md.trr -s md.tpr -mc Program didn't write the mc.xvg Average translational dipole moment is zero. Average translational dipole moment M_J [enm] after 15001 frames (|M|^2): -0.00 -0.00 -0.00 (0.00) Can you tell where is the problem? Nilesh Hi, I am using the release branch of 4.5. /Flo --- Florian Dommert Dipl. Phys. Institut für Computerphysik Universität Stuttgart Allmandring 3 D-70569 Stuttgart Tel.: 0711-68563613 Fax: 0711-68563658 -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Montag, 25. Februar 2013 15:35 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: [gmx-users] g_current Hello, Thanks. I will update Gromacs version. Can you tell which version you are using ? Nilesh Hi, Can you update your Gromacs version to an actual release and check if the problem still occurs. It is very strange that the Einstein-Helfand fit gives 0 for sigma and M_J^2. Cheers, Flo --- Florian Dommert Dipl. Phys. Institut für Computerphysik
[gmx-users] Re: RDF calculation
Dear all I have two discrete residues which are being connected together by sulfur atom in each residue. I need to find how the density varies around the residues or atoms attached with the sulfur atom and the water molecules surrounding it. for that I created a group by selecting the two sulfur atoms using the index file. By giving RDF command Can I select the group which I created by index file as first group and the system as second group. And also is it possible to have RDF for vacuum phase simulation. Thanks in Advance KEERTHANA -- 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] reg binding free energy
On Mar 7, 2013, at 2:59 AM, Justin Lemkul wrote: On 3/6/13 8:57 PM, Vishwambhar Bhandare wrote: dear gromacs user, how i can do binding free energy calculation for RNA duplex in gromacs? any tutorial for the same?? Free energy calculations involving interactions between macromolecules are typically done with umbrella sampling. A tutorial is linked from gromacs.org, otherwise refer to the literature for suggested methodology. The challenge is likely to find a proper reaction coordinate and assure that you sample sufficiently along it. You may end up wasting a lot of computer time if you make a poor choice. Erik -- 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: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
On Wed, 6 Mar 2013, Christoph Junghans wrote: I had a another look at the issue and I guess cmake's blas detention is a bit flaky, when it comes to static libraries. You are using liblapack.a, which has no link information, with liblapack.so it should have worked. Anyhow, thanks for reporting the issue. There is no liblapack.so with ATLAS? Anyway, I tried to explain the issues more clearly below. I am not going to insist but it would be nice to be able to use the ATLAS library I guess... :) The following library files are available with ATLAS and your cmake config checks use f77blas;atlas libatlas.a libcblas.a libf77blas.a liblapack.a libptcblas.a libptf77blas.a libsatlas.so libtatlas.so At: http://ac-archive.sourceforge.net/ac-archive/acx_blas.html It says that you will have to use the same FORTRAN compiler to link ATLAS. However your checker is using gcc to check linking. So the first bug is because the checker is trying to link f77blas with gcc. This requires -lgfortran. You can see many related information if you do a web search for undefined reference to `_gfortran_st_write'). Otherwise you should use gfortran for the tests. Therefore it is impossible for gromacs to use ATLAS library. The second problem is because f77blas;atlas should include cblas for linking. Again, at the example which is present at: http://ac-archive.sourceforge.net/ac-archive/acx_blas.html BLAS_LIBS=-lcblas -lf77blas -latlas is used. Therefore it is again impossible to find ATLAS library even when it exists. The third problem is ambiguity in the manual at: http://www.gromacs.org/Documentation/Installation_Instructions#4.1._Configuring_with_CMake It says: A key thing to consider here is the setting of CMAKE_INSTALL_PREFIX. However it is not clear what 'setting' means in here. (Being unfamiliar with cmake, I defaulted to setting it in the environment which was wrong) Later I found out CMAKE_INSTALL_PREFIX can only be used as a cmake variable (not set in environment). But DESTDIR should be set for setting installation prefix instead ? See: http://www.cmake.org/cmake/help/v2.8.8/cmake.html#variable%3aCMAKE_INSTALL_PREFIX http://www.cmake.org/Wiki/CMake_FAQ#Does_CMake.27s_.22make_install.22_support_DESTDIR.3F I hope the problems in ATLAS detection and documentation would be fixed. Thanks for your interest in these small issues. Thanks, Evren -- 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: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
Hi, Note that the linear algebra in Gromacs is limited to eigenvalue solving in two analysis tools, the MD engine does not use any (large) linear algebra. So linear algebra library performance is irrelevant, except for the cases where users would want to repeated uses one of the two tools with large systems. Even then, our built-in code is not bad. Cheers, Berk Date: Thu, 7 Mar 2013 11:27:27 +0200 From: eyurt...@abo.fi To: jungh...@votca.org CC: gmx-users@gromacs.org Subject: [gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems... On Wed, 6 Mar 2013, Christoph Junghans wrote: I had a another look at the issue and I guess cmake's blas detention is a bit flaky, when it comes to static libraries. You are using liblapack.a, which has no link information, with liblapack.so it should have worked. Anyhow, thanks for reporting the issue. There is no liblapack.so with ATLAS? Anyway, I tried to explain the issues more clearly below. I am not going to insist but it would be nice to be able to use the ATLAS library I guess... :) The following library files are available with ATLAS and your cmake config checks use f77blas;atlas libatlas.a libcblas.a libf77blas.a liblapack.a libptcblas.a libptf77blas.a libsatlas.so libtatlas.so At: http://ac-archive.sourceforge.net/ac-archive/acx_blas.html It says that you will have to use the same FORTRAN compiler to link ATLAS. However your checker is using gcc to check linking. So the first bug is because the checker is trying to link f77blas with gcc. This requires -lgfortran. You can see many related information if you do a web search for undefined reference to `_gfortran_st_write'). Otherwise you should use gfortran for the tests. Therefore it is impossible for gromacs to use ATLAS library. The second problem is because f77blas;atlas should include cblas for linking. Again, at the example which is present at: http://ac-archive.sourceforge.net/ac-archive/acx_blas.html BLAS_LIBS=-lcblas -lf77blas -latlas is used. Therefore it is again impossible to find ATLAS library even when it exists. The third problem is ambiguity in the manual at: http://www.gromacs.org/Documentation/Installation_Instructions#4.1._Configuring_with_CMake It says: A key thing to consider here is the setting of CMAKE_INSTALL_PREFIX. However it is not clear what 'setting' means in here. (Being unfamiliar with cmake, I defaulted to setting it in the environment which was wrong) Later I found out CMAKE_INSTALL_PREFIX can only be used as a cmake variable (not set in environment). But DESTDIR should be set for setting installation prefix instead ? See: http://www.cmake.org/cmake/help/v2.8.8/cmake.html#variable%3aCMAKE_INSTALL_PREFIX http://www.cmake.org/Wiki/CMake_FAQ#Does_CMake.27s_.22make_install.22_support_DESTDIR.3F I hope the problems in ATLAS detection and documentation would be fixed. Thanks for your interest in these small issues. Thanks, Evren -- 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
[gmx-users] Hamiltonian replica exchange umbrella sampling with gmx 4.6
Dear gmx-users, I am currently trying to runt Hamiltonian replica exchange umbrella sampling in hope to do some better sampling. I have generated a number of tpr-files along my reaction coordinate and they all run fine in independent simulations. The issue comes when I would like the replica exchange to start. The following line is used to initiate the exchange: mdrun_mpi -replex 1000 -s md -pf pullf -px pullx -multi 40 -maxh 0.5 All replicas have the same temperature and the following error is what I face seconds after submitting the job: The properties of the 40 systems are all the same, there is nothing to exchange For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I could simply change the temperature between the replicas by 0.001 K and it would run I think. But that is not very elegant. Does anyone have any suggestions? Thanks in advance! Best regards, Joakim-- 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: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
On Thu, 7 Mar 2013, Berk Hess wrote: Hi, Note that the linear algebra in Gromacs is limited to eigenvalue solving in two analysis tools, the MD engine does not use any (large) linear algebra. So linear algebra library performance is irrelevant, except for the cases where users would want to repeated uses one of the two tools with large systems. Even then, our built-in code is not bad. Cheers, Berk Hello, I am not sure what you are suggesting as a fix to the problem? Do you mean the support for ATLAS should/will be removed as a fix because it is not very useful performancewise (and non-functional) anyway? Thanks, Evren -- 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: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
Hi, This was only a note, not a fix. I was just trying to say that what linear algebra library you use for Gromacs is irrelevant in more than 99% of the cases. But having said that, the choice of library should not complicate the configure stage of Gromacs. Cheers, Berk Date: Thu, 7 Mar 2013 14:54:39 +0200 From: eyurt...@abo.fi To: gmx-users@gromacs.org Subject: RE: [gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems... On Thu, 7 Mar 2013, Berk Hess wrote: Hi, Note that the linear algebra in Gromacs is limited to eigenvalue solving in two analysis tools, the MD engine does not use any (large) linear algebra. So linear algebra library performance is irrelevant, except for the cases where users would want to repeated uses one of the two tools with large systems. Even then, our built-in code is not bad. Cheers, Berk Hello, I am not sure what you are suggesting as a fix to the problem? Do you mean the support for ATLAS should/will be removed as a fix because it is not very useful performancewise (and non-functional) anyway? Thanks, Evren -- 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
[gmx-users] question on RDF
Dear all, When calculation the RDF, it asks: Select a reference group and 1 group Group 0 ( System) has 1600 elements Group 1 ( Other) has 1600 elements Group 2 ( PE) has 1600 elements Group 3 ( a_1-1600) has 1600 elements My question is what's the difference between reference group and 1 group, how the RDF calculated for them. Thank you very much. Kind regards, Li -- 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] Hamiltonian replica exchange umbrella sampling with gmx 4.6
Hi, Joakim- Hamiltonian exchange only should work if there is a lambda coupling parameter that defines the potential at each state. You need to define your pulling potential so that the coupling-lambda parameter can be used to define the different pulling location centers along your trajectory. Does this make it clearer? On Thu, Mar 7, 2013 at 7:26 AM, Joakim Jämbeck jamb...@me.com wrote: Dear gmx-users, I am currently trying to runt Hamiltonian replica exchange umbrella sampling in hope to do some better sampling. I have generated a number of tpr-files along my reaction coordinate and they all run fine in independent simulations. The issue comes when I would like the replica exchange to start. The following line is used to initiate the exchange: mdrun_mpi -replex 1000 -s md -pf pullf -px pullx -multi 40 -maxh 0.5 All replicas have the same temperature and the following error is what I face seconds after submitting the job: The properties of the 40 systems are all the same, there is nothing to exchange For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I could simply change the temperature between the replicas by 0.001 K and it would run I think. But that is not very elegant. Does anyone have any suggestions? Thanks in advance! Best regards, Joakim-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
On Thu, Mar 7, 2013 at 2:02 PM, Berk Hess g...@hotmail.com wrote: Hi, This was only a note, not a fix. I was just trying to say that what linear algebra library you use for Gromacs is irrelevant in more than 99% of the cases. But having said that, the choice of library should not complicate the configure stage of Gromacs. I guess Evren assumed that GROMACS has an explicit dependency on an external linear algebra library. To be concrete, you can simply use the GROMACS internal linear algebra code by setting -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF. -- Szilárd PS: This issue sounds like a valid reason to consider switching external BLAS/LAPACK off by default. Cheers, Berk Date: Thu, 7 Mar 2013 14:54:39 +0200 From: eyurt...@abo.fi To: gmx-users@gromacs.org Subject: RE: [gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems... On Thu, 7 Mar 2013, Berk Hess wrote: Hi, Note that the linear algebra in Gromacs is limited to eigenvalue solving in two analysis tools, the MD engine does not use any (large) linear algebra. So linear algebra library performance is irrelevant, except for the cases where users would want to repeated uses one of the two tools with large systems. Even then, our built-in code is not bad. Cheers, Berk Hello, I am not sure what you are suggesting as a fix to the problem? Do you mean the support for ATLAS should/will be removed as a fix because it is not very useful performancewise (and non-functional) anyway? Thanks, Evren -- 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 -- 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: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
On Thu, 7 Mar 2013, Szilárd Páll wrote: On Thu, Mar 7, 2013 at 2:02 PM, Berk Hess g...@hotmail.com wrote: Hi, This was only a note, not a fix. I was just trying to say that what linear algebra library you use for Gromacs is irrelevant in more than 99% of the cases. But having said that, the choice of library should not complicate the configure stage of Gromacs. I guess Evren assumed that GROMACS has an explicit dependency on an external linear algebra library. To be concrete, you can simply use the GROMACS internal linear algebra code by setting -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF. -- Szilárd PS: This issue sounds like a valid reason to consider switching external BLAS/LAPACK off by default. I actually saw that the configure said it will use internal blas/lapack. I also understand that the blas/lapack is not very relevant for gromacs. But none of these mean there is not a problem. (which is probably easy to fix anyway). In either case, I reported it so developers can be informed and I dont mind if it is fixed or not. But thanks for the feedback and information given. Thanks Evren -- 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] electron desnity
Hello In the g_density manual it is mentioned that When calculating electron densities, atomnames are used instead of types, this is bad So what should be included in the electrons.dat file. The unique atomtypes of the group or all the atomnames of this group? Thanks in advance. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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] Small bug with -pi in g_mindist?
On 2013-03-07 19:02, Reid Van Lehn wrote: Hi users, I was experimenting with using a hexagonal unit cell for a lipid membrane system by building a box with vectors A A C (i.e. two equivalent vectors in the xy plane and distinct z vector) and angles 90 90 60, which is correctly represented as hexagonal after converting with trjconv. I equilibrated this box and a system with the same number of lipids and water molecules but in a rectangular box. I confirmed that after equilibration the area per lipid for each system is the same, and after visualization confirmed that the hexagonal system and rectangular system occupied about the same area (of course subject to fluctuations). For a hexagon and square of equivalent area, the minimum distance between periodic images should be 1/sqrt( sin 60 degrees) = ~1.075 times larger for the hexagon than in the square case if I worked out the geometry correctly. To test to make sure I had the correct new minimum distance, I ran g_mindist -pi with both a single atom and a single water molecule from the simulation box after resizing the Z axis to a large value, restricting the minimum distance between periodic images to only the xy plane. Surprisingly, the result came out as smaller than the equivalent minimum distance in the rectangular box, and was equal to the box vector B. Since in GMX box vectors are stored in the .gro file in a 3x3 matrix, the box[YY][YY] vector for an ab angle of 60 degrees was (correctly) equal to sin 60 * the A vector. However, the correct periodic distance should have been the A vector, which again was correctly ~1.075 * the box vector in the rectangular box by comparing the .gro files. I believe that this is a small bug in g_mindist, and found the source: on lines 71 and 92 of gmx_mindist.c (version 4.6), the initial minimum distance is set based on the minimum of the box[XX][XX], box[YY][YY], and box[ZZ][ZZ] vectors. I think this is fine for rectangular boxes, but fails for triclinic boxes with box angles differing from 90 degrees. In my particular case of a hexagonal xy plane, the box[YY][YY] vector is shorter than the box[XX][XX] vector by a factor of sin 60, but this is not actual the shortest distance. Explicitly printing out the distances calculated between periodic images in the current version of the code for both a single atom and a water molecule confirms that the minimum distance is the box[XX][XX] vector. Thanks for reporting and giving a solution. http://redmine.gromacs.org/issues/1183 A fix for this was substituting norm(box[0]), norm(box[1]), and norm(box[2]) for the box[XX][XX] etc. vectors in line 71, as then the minimum was properly set. I realize this is a bug that is unlikely to affect many users, but given the prevalence of non-rectangular boxes and the observation of previous complaints about mindist in the user list, I thought it would be good to report. Please let me know if I made an error anywhere! Best, Reid -- 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] X particles communicated to PME node Y are more ...
2013/3/4 Justin Lemkul jalem...@vt.edu Dear Justin, With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1 If you find something weird in the mdp file or require further explanations on the points do mention I will do my best to provide the necessary info. Right below are the comments: In that case, it's probably something worth pursuing. Having the new version fail when an older version works is curious. Can you please provide all of the following details: 1. Compilers used to build Gromacs 2. Hardware description These lines are from the CMakeOutput.log file: The system is: Linux - 2.6.32-5-amd64 - x86_64(*) Compiling the C compiler identification source file CMakeCCompilerId.c succeeded. Compiler: /usr/bin/gcc cc -v: gcc version 4.4.5 3. mdrun command 4. Complete .mdp file grompp -f minimize.mdp -c Mut3.gro -o em.tpr -p topol.top mdrun -v -deffnm em The minimize.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5 nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 pbc = xyz Thank-you a lot for all your tips and comments, Miguel -Justin 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote: I have tried the same issue (same system with same mdp file and same initial configuration as starting structure) and is running without any problems with GROMACS-4.5.5. Anyone knows what is happening? You didn't tell us your Gromacs version in the previous post so the best guess is random bug that was somehow fixed before 4.5.5. -Justin 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. Changing them will actually increase your likelihood of failure. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn-- Lys mutation. Any hint to solve the error? If EM stops at the first step, there's usually something catastrophically wrong with the starting configuration. If you've decreased the value of emstep, there's little else that will account for such behavior. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Topology of Graphite Oxide
On 3/7/13 3:36 AM, zhhxu wrote: Hi users: I want to run a simulation of adsorption of protein on graphite oxide(GO) which is oxidized at random and is near 80% coverage by hydroxyl and epoxyl group. My first question is how to generate a topology filefor GO. Previous to search solution to this problem in this forum, I had tried to make a topology for GO use g_x2top with command: g_x2top -f input.pdb -nopbc -r outputname -o outputname. But g_x2top did not work fine(fine for prestine graphite) and gave error messages like Can not find forcefield for atom .. The .n2t files provided with the (few) force fields in Gromacs are rather inflexible, so you will probably need to modify them to suit your needs. My second also is about definition of improper dihedral in opls-aa. Whether it is validate to assign a improper dihedral for a central sp2 carbon atom with three other bonded atoms no matter of what is type of other three atom? I have gotten (mentioned above) a topology file of pristine graphite for opls-aa with g_x2top(the command is similar to above), but the topology file did not include any improper dihedral. g_x2top doesn't write impropers, so you have to manually add them if needed. Assignment of proper parameters should be done based on analogous functional groups present in the force field or by a suitable derivation protocol. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: RDF calculation
On 3/7/13 3:54 AM, Keerthana S.P Periasamy wrote: Dear all I have two discrete residues which are being connected together by sulfur atom in each residue. I need to find how the density varies around the residues or atoms attached with the sulfur atom and the water molecules surrounding it. for that I created a group by selecting the two sulfur atoms using the index file. By giving RDF command Can I select the group which I created by index file as first group and the system as second group. And also is it possible to have RDF for vacuum phase simulation. Thanks in Advance You can select any groups you want for RDF calculations, around any central reference group you like. You can probably do in vacuo RDF, though you probably have to use -nopbc. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Special bonds with terminal residue
On 3/7/13 5:44 AM, Baptiste Demoulin wrote: Hello Gromacs users, I try to link a metallic core to its surrounding amino-acids. Everything works find for bonding side chains and metal atoms, but I have troubles when it comes to bonding COO- group from a terminus ALA. The error printed by pdb2gmx is the following : Program pdb2gmx, VERSION 4.6 Source code file: /home1/retegan/software/gromacs-4.6/src/kernel/pgutil.c, line: 126 Fatal error: Residue 334 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type special bond in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Here my specbon.dat file : 22 CYS SG 1 CYS SG 1 0.2 CYS2CYS2 CYS SG 1 HEM FE 2 0.25CYS2HEME CYS SG 1 HEM CAB 1 0.18CYS2HEME CYS SG 1 HEM CAC 1 0.18CYS2HEME MET SD 1 HEM FE 1 0.24MET HEME CO C 1 HEMEFE 1 0.19CO HEME CYM SG 1 CYM SG 1 0.2 CYS2CYS2 HIS NE2 1 FE2 FE 4 0.23HID FE2 HIS NE2 1 OEX MN1 6 0.21HID OEX ASP OD2 1 OEX MN1 6 0.23ASP OEX GLU OE2 1 OEX MN1 6 0.20GLU OEX GLU OE1 1 OEX MN2 6 0.21GLU OEX ASP OD1 1 OEX MN2 6 0.21ASP OEX ALA OXT 1 OEX MN2 6 0.20ALA OEX GLU OE1 1 OEX MN3 6 0.21GLU OEX GLU OE2 1 OEX MN3 6 0.23GLU OEX SOX O 1 OEX MN4 6 0.21SOX OEX ASP OD2 1 OEX MN4 6 0.21ASP OEX GLU OE2 1 OEX MN4 6 0.22GLU OEX SOX O 1 OEX CA1 6 0.25SOX OEX ALA O 1 OEX CA1 6 0.25ALA OEX I tried to change the atom names within specbond.dat, in the initial pdb file, but nothing has worked yet... Does someone have an idea of what is going on ? Terminal oxygens are renamed according to the specifications in the relevant .c.tdb file. A terminal residue has no atom named O since the name is changed. If only one bond is missing, it's probably easiest to just manually add it to the topology, otherwise remove the offending line in specbond.dat, see how the terminal oxygens are renamed, and then try using the relevant atom name(s) for creating your bonds. If that approach doesn't work, then the only option is manual addition to the topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question on RDF
On 3/7/13 8:31 AM, l@utwente.nl wrote: Dear all, When calculation the RDF, it asks: Select a reference group and 1 group Group 0 ( System) has 1600 elements Group 1 ( Other) has 1600 elements Group 2 ( PE) has 1600 elements Group 3 ( a_1-1600) has 1600 elements My question is what's the difference between reference group and 1 group, how the RDF calculated for them. Please refer to the manual for the discussion of how RDF is calculated. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Use dihedraltype 4 to allow several multiplicity terms
On 3/7/13 10:46 AM, Steven Neumann wrote: Dear Gmx Users, I used charmm server to get the parameters for my new molecule - alkane. i converted it into the gromacs topology. When I try grompp: WARNING 1 [file ffbonded.itp, line 7948]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159787 2 0 0.159787 2 new: CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 WARNING 2 [file ffbonded.itp, line 7949]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159829 2 0 0.159829 2 new: CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 My ffnonbonded.itp corresponding lines: [ dihedraltypes ] ; i j k l funcphi0cp mult CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 Can you please explain me this? Shall use 4 instead of 2 or 6 at the end of these lines? No, the last entries are the multiplicity, not the function type (which is the fifth entry, under func). Unfortunately, I cannot answer why grompp is prompting you to use type 4, which according to the manual is for periodic improper dihedrals, not proper dihedrals. Maybe you've added those lines in the wrong directive, i.e. with impropers rather than propers? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron desnity
On 3/7/13 11:14 AM, George Patargias wrote: Hello In the g_density manual it is mentioned that When calculating electron densities, atomnames are used instead of types, this is bad So what should be included in the electrons.dat file. The unique atomtypes of the group or all the atomnames of this group? There is a very primitive example of what the electrons.dat file should look like in the help description. You should use atom names, not types, just as the message says. Each line describes the number of atoms around each atom, not groups of atoms. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Use dihedraltype 4 to allow several multiplicity terms
Hello Steven, I would suggest you to look if this angle is not defined somewhere else in your file. Indeed, it seems that the program has another value for this. The 2 and 6 at the end of the line are the multiplicity, so they don't need to be changed. The relevant value is the one indicated in the 'func' column. 9 should be ok, since it describes a function of several Fourier term. I don't understand why grompp propose to chage this to 4... Baptiste 2013/3/7 Steven Neumann s.neuman...@gmail.com Dear Gmx Users, I used charmm server to get the parameters for my new molecule - alkane. i converted it into the gromacs topology. When I try grompp: WARNING 1 [file ffbonded.itp, line 7948]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159787 2 0 0.159787 2 new: CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 WARNING 2 [file ffbonded.itp, line 7949]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159829 2 0 0.159829 2 new: CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 My ffnonbonded.itp corresponding lines: [ dihedraltypes ] ; i j k l funcphi0cp mult CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 Can you please explain me this? Shall use 4 instead of 2 or 6 at the end of these lines? I am using Gromacs 4.5.5 Stevem -- 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] X particles communicated to PME node Y are more ...
On 3/7/13 1:17 PM, Miguel Ángel Mompeán García wrote: 2013/3/4 Justin Lemkul jalem...@vt.edu Dear Justin, With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1 If you find something weird in the mdp file or require further explanations on the points do mention I will do my best to provide the necessary info. Right below are the comments: In that case, it's probably something worth pursuing. Having the new version fail when an older version works is curious. Can you please provide all of the following details: 1. Compilers used to build Gromacs 2. Hardware description These lines are from the CMakeOutput.log file: The system is: Linux - 2.6.32-5-amd64 - x86_64(*) Compiling the C compiler identification source file CMakeCCompilerId.c succeeded. Compiler: /usr/bin/gcc cc -v: gcc version 4.4.5 3. mdrun command 4. Complete .mdp file grompp -f minimize.mdp -c Mut3.gro -o em.tpr -p topol.top mdrun -v -deffnm em The minimize.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5 nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 pbc = xyz Does the .tpr file run on a machine with different hardware or compilers? The GCC version is outdated, though in principle should work fine. If the failure consistently happens on your machine (and especially if it happens on other machines), please file a bug report on redmine.gromacs.org and include a .tpr file and all of the information posted above. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: electron desnity
Hello In the g_density manual it is mentioned that When calculating electron densities, atomnames are used instead of types, this is bad So what should be included in the electrons.dat file. The unique atomtypes of the group or all the atomnames of this group? Thanks in advance. I am not 100% sure, but it probably reads atom names and tries to guess the element based on the first two symbols. Vitaly Chaban -- 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: Hamiltonian replica exchange umbrella sampling with gmx 4.6
Dear Michael, Thank you for your reply. Yes, it is relatively clear now. Will try to play around with this later today. Best, Joakim Date: Thu, 7 Mar 2013 08:55:31 -0500 From: Michael Shirts mrshi...@gmail.com Subject: Re: [gmx-users] Hamiltonian replica exchange umbrella sampling with gmx 4.6 To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, Joakim- Hamiltonian exchange only should work if there is a lambda coupling parameter that defines the potential at each state. You need to define your pulling potential so that the coupling-lambda parameter can be used to define the different pulling location centers along your trajectory. Does this make it clearer? -- 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
