[gmx-users] A simple question
Hi, everyone. I am running gromacs, using force field G43a2. I just want to make sure that, does the gromacs uses periodic boundary condition in my simulation? Well, anyhow, where could I find a place to know what kind of boundary condition the gromacs uses? Thanks ahead. Xiaoling Leng -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] A simple question
Manual section 7.3 covers what all the of the .mdp settings do. One of them covers PBC. Mark - Original Message - From: Xiaoling Leng Date: Thursday, October 7, 2010 18:22 Subject: [gmx-users] A simple question To: gmx-users > Hi, everyone. I am running gromacs, using force field G43a2. I just want to > make sure that, does the gromacs uses periodic boundary condition in my > simulation? Well, anyhow, where could I find a place to know what kind of > boundary condition the gromacs uses? > > Thanks ahead.> > Xiaoling Leng > -- > 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: Problem with pressure coupling
On Wed, Sep 29, 2010 at 21:56, David van der Spoel wrote: > > After setting nstcalcenergy = 1 I get > Density 996.894 1.2 3.85083 1.86718 (kg/m^3) > > In other words the bug can be circumvented by setting this variable to 1. I > will file a bugzilla. > Is this bug in now? I can't find it in recent bugs, but perhaps I've missed it. If it is not in, should I file it? Regards, Ondrej -- 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] best parameters for energy determination with GBSA
Dear GROMACS users, I try to compute energies of a small peptide-domain complex and of its constituents using implicit solvent, so that I can get the binding Delta E. I need the accuracy to be high enough so that I can reliably measure the Delta Delta E between the wildtype peptide and a mutation of it. I would like to get advice as to the best setting and parameters to use; are the ones given below the correct and best ones (most in an mdp file, some run control parameters of GROMACS commands)? Are other defaults in need to be changed? As the GBSA method necessitates using the inexact cut-off interactions, and my system is rather small, I consider using no cut-off at all, i.e. an all-vs.-all approach. For that I understand the parameters should be nstlist=0 ns_type=simple -pd ; in mdrun coulombtype=cut-off rcoulomb=0 vdwtype=cut-off rvdw=0 rlist=0 Then, there are the implicit solvent parameters themselves: implicit_solvent=GBSA gb_algorithm= Still sa_algorithm=Ace-approximation rgbradii=0 Finally, regarding the simulation box, I see no need for periodic boundary conditions, and I pick some big margin around the system (as there are no water molecules, no need to spare): pbc=no -d 5.0 ; in editconf What do you say? Thanks, Ehud. -- 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: Problem with pressure coupling
Ondrej Marsalek wrote: On Wed, Sep 29, 2010 at 21:56, David van der Spoel wrote: After setting nstcalcenergy = 1 I get Density996.8941.23.850831.86718 (kg/m^3) In other words the bug can be circumvented by setting this variable to 1. I will file a bugzilla. Is this bug in now? I can't find it in recent bugs, but perhaps I've missed it. If it is not in, should I file it? http://bugzilla.gromacs.org/show_bug.cgi?id=579 -Justin Regards, Ondrej -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Re: Problem with pressure coupling
Hi, It's bugzilla 579: http://bugzilla.gromacs.org/show_bug.cgi?id=579 Actually the title is wrong, the pressure was correct, the pressure scaling, and thus the density, not. Berk > Date: Thu, 7 Oct 2010 12:28:15 +0200 > Subject: Re: [gmx-users] Re: Problem with pressure coupling > From: ondrej.marsa...@gmail.com > To: gmx-users@gromacs.org > > On Wed, Sep 29, 2010 at 21:56, David van der Spoel > wrote: > > > > After setting nstcalcenergy = 1 I get > > Density996.8941.23.850831.86718 (kg/m^3) > > > > In other words the bug can be circumvented by setting this variable to 1. I > > will file a bugzilla. > > > > Is this bug in now? I can't find it in recent bugs, but perhaps I've > missed it. If it is not in, should I file it? > > Regards, > Ondrej > -- > 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: Problem with pressure coupling
Hi, thanks for fixing this, Berk. Silly me, I did not include RESOLVED bugs in my original search and therefore missed it. Ondrej On Thu, Oct 7, 2010 at 12:38, Berk Hess wrote: > Hi, > > It's bugzilla 579: > http://bugzilla.gromacs.org/show_bug.cgi?id=579 > Actually the title is wrong, the pressure was correct, the pressure scaling, > and thus the density, not. > > Berk > >> Date: Thu, 7 Oct 2010 12:28:15 +0200 >> Subject: Re: [gmx-users] Re: Problem with pressure coupling >> From: ondrej.marsa...@gmail.com >> To: gmx-users@gromacs.org >> >> On Wed, Sep 29, 2010 at 21:56, David van der Spoel >> wrote: >> > >> > After setting nstcalcenergy = 1 I get >> > Density 996.894 1.2 3.85083 1.86718 (kg/m^3) >> > >> > In other words the bug can be circumvented by setting this variable to >> > 1. I >> > will file a bugzilla. >> > >> >> Is this bug in now? I can't find it in recent bugs, but perhaps I've >> missed it. If it is not in, should I file it? >> >> Regards, >> Ondrej >> -- >> 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 list gmx-us...@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: Problem with pressure coupling
Well, this happens to everybody. The search feature is bugzilla is far too complex. We are considering switching to a more powerful and easier system. Berk > Date: Thu, 7 Oct 2010 12:41:17 +0200 > Subject: Re: [gmx-users] Re: Problem with pressure coupling > From: ondrej.marsa...@gmail.com > To: gmx-users@gromacs.org > > Hi, > > thanks for fixing this, Berk. Silly me, I did not include RESOLVED > bugs in my original search and therefore missed it. > > Ondrej > > > On Thu, Oct 7, 2010 at 12:38, Berk Hess wrote: > > Hi, > > > > It's bugzilla 579: > > http://bugzilla.gromacs.org/show_bug.cgi?id=579 > > Actually the title is wrong, the pressure was correct, the pressure scaling, > > and thus the density, not. > > > > Berk > > > >> Date: Thu, 7 Oct 2010 12:28:15 +0200 > >> Subject: Re: [gmx-users] Re: Problem with pressure coupling > >> From: ondrej.marsa...@gmail.com > >> To: gmx-users@gromacs.org > >> > >> On Wed, Sep 29, 2010 at 21:56, David van der Spoel > >> wrote: > >> > > >> > After setting nstcalcenergy = 1 I get > >> > Density996.8941.23.850831.86718 (kg/m^3) > >> > > >> > In other words the bug can be circumvented by setting this variable to > >> > 1. I > >> > will file a bugzilla. > >> > > >> > >> Is this bug in now? I can't find it in recent bugs, but perhaps I've > >> missed it. If it is not in, should I file it? > >> > >> Regards, > >> Ondrej > >> -- > >> 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 -- 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] best parameters for energy determination with GBSA
Hi Ehud! Your settings are correct. However, you can also use domain decomposition with GB, and I at least usually bypass the editconf stage, and do pdb2gmx->grompp->mdrun, when you do not want any pbc. /Per 7 okt 2010 kl. 12.29 skrev Ehud Schreiber: > Dear GROMACS users, > > I try to compute energies of a small peptide-domain complex and of its > constituents using implicit solvent, so that I can get the binding Delta E. I > need the accuracy to be high enough so that I can reliably measure the Delta > Delta E between the wildtype peptide and a mutation of it. > > I would like to get advice as to the best setting and parameters to use; are > the ones given below the correct and best ones (most in an mdp file, some run > control parameters of GROMACS commands)? Are other defaults in need to be > changed? > > As the GBSA method necessitates using the inexact cut-off interactions, and > my system is rather small, I consider using no cut-off at all, i.e. an > all-vs.-all approach. For that I understand the parameters should be > nstlist=0 > ns_type=simple > -pd ; in mdrun > coulombtype=cut-off > rcoulomb=0 > vdwtype=cut-off > rvdw=0 > rlist=0 > > Then, there are the implicit solvent parameters themselves: > implicit_solvent=GBSA > gb_algorithm= Still > sa_algorithm=Ace-approximation > rgbradii=0 > > Finally, regarding the simulation box, I see no need for periodic boundary > conditions, and I pick some big margin around the system (as there are no > water molecules, no need to spare): > pbc=no > -d 5.0 ; in editconf > > What do you say? > > Thanks, > Ehud. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Self Diffusion contant
Dear Gromacs, I have been calculating the self Diffusion constant of my system. Surfactants in a different solvents of the same volume. After simulation for 20ns I found the following data for the trajectory of the mean square displacement. # D[ TPA] = 0.2039 (+/- 0.0503) (1e-5 cm^2/s) 0 0 2 0.0105286 4 0.0162435 6 0.0212711 80.026031 10 0.0307584 120.035134 14 0.0393323 16 0.0434628 18 0.0475354 20 0.0516609 - - - - - - 920 1.16467 922 1.16756 924 1.1703 926 1.17267 928 1.17383 930 1.17483 932 1.17581 934 1.17754 936 1.17957 938 1.18199 940 1.1829 942 1.18596 944 1.18871 946 1.19099 948 1.19219 950 1.19321 952 1.19445 954 1.19613 956 1.19838 - - - - - - 10576 11.7747 10578 11.785 10580 11.7817 10582 11.7833 10584 11.7847 10586 11.784 10588 11.7855 10590 11.7904 10592 11.7926 10594 11.7943 10596 11.8036 10598 11.8141 10600 11.8112 - - - - - - 19960 36.4106 19962 36.2607 19964 39.9243 19966 39.7493 19968 39.6744 19970 39.5838 19972 39.6723 19974 39.6374 19976 39.518 19978 39.4935 19980 39.3834 19982 39.1136 19984 42.3888 19986 42.168 19988 42.1337 19990 41.9395 19992 42.0065 19994 42.0993 19996 41.8652 19998 41.8419 2 41.9419 20002 41.6049 From my data, the graph shows a linear trend until 18ns but as soon as it reaches around 19, 20ns it dramatically increases the MSD value. Since the surfactants form aggregation I was expecting the MSD curve to go down. Is any explanation for that. Why? suddenly increases the MSD curve. Which is then the correct slop then! Thank you Rob Quoting "Justin A. Lemkul" : Paymon Pirzadeh wrote: I assumption was that when provide the index file, do_dssp will do the analysis for the protein but prints out the results only for the designated residues. All I wanted was a better resolution on the final When prompted for only one group, that group is used for calculation and output. xpm plot to see the secondary structure of the protein at those residues of interest. Any suggestions on how we can increase the resolution of dssp plot and enlarging the axis of residues? Yes, use an .m2p file to adjust the matrix spacing. This was discussed several days ago. By the way, what would the option -nice do here? Likely nothing. Nice levels are irrelevant for most tasks. -Justin Paymon On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Justin, I produced the index file based on your suggestion, but when I ran the do_dssp, a completely different result was spit out comparing to what the whole protein analysis had given. Any ideas on why that might have happened? That depends on what "completely different" means. I have no idea. If you're only analyzing a subset of the residues, you're going to get a discontinuous plot that's probably going to look a whole lot different from any analysis done on the whole protein. What's more, if you're only considering small fragments of the protein, then omitting surrounding residues from the analysis probably won't permit DSSP to find hydrogen bonding partners that are necessary to determine the correct secondary structure. -Justin Paymon On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Hello, I want to check the secondary structure of protein at particular residues. Since dssp needs all main chain atoms, does the following command at the make_ndx prompt makes the correct index file? You can answer that yourself by looking at the resulting index file. 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 To get these groups to merge, I think you probably need to do 5 & r 1 | ... -Justin (Main chain atom of particular residues). regards, Paymon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department
[gmx-users] forces from trajectory
Hi In the post-processing ( analysis) code using gromacs trajectory, I access force values on atom using fr.x[indx_atm][XX]. The confusion I have is that " what force is it? is it the force before constraints ( fixed bonds) are applied or is it the effective force due to atom-atom interactions plus any constraints?" thanks sikandar -- 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] SwissParam
Dear Gromacs users, This is an announcement for SwissParam, a web service that provides topologies and parameters for small organic molecules, compatible with the CHARMM all atoms force field, for use with the CHARMM or GROMACS softwares: http://swissparam.ch/ The server is fully automatic, and the user only needs to provide the organic molecule of interest in the mol2 format. Topology and parameter files are sent back by e-mail, generally within minutes. For GROMACS users, an itp file is generated for the small molecule, which must be included to the protein or DNA topology produced by GROMACS. A tutorial page explains step by step how to set up a protein-ligand system. Force field parameters are derived from the Merck Molecular ForceField (MMFF). Dihedral angle terms are taken as is, while only the harmonic part of the bond, angle and improper terms are retained (the quartic part is discarded). Charges are taken from MMFF. Van der Waals parameters are taken from the closest atom type in CHARMM22. The service is intended for fast and easy force field generation. The parameters have been tested in "drug design" type of calculations, like docking, minimizations, rapid binding energy estimation (LIECE, MMGB/SA), etc... Deeper parameterizations are probably required for applications in which a finer description of the molecule is required, (e.g. normal mode calculations, ...). SwissParam results can then be used as a starting point for such a procedure. Enjoy SwissParam, and please notify us of any question or suggestion for improvement. Try SwissParam now !! Best regards, Michel Cuendet == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland http://lausanne.isb-sib.ch/~mcuendet/ == -- 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] Simulations on GPU
Hi, On 10/6/10 3:48 AM, Igor Leontyev wrote: Szilárd wrote: The beta versions are all outdated, could you please use the latest source distribution (4.5.1) instead (or git from the release-4-5-patches branch)? The result is the same for both the distribution 4.5.1 and git from the release-4-5-patches. See the output bellow. = PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64: CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include -I//usr/local/opt/bin/mpi/openmpi-1.4.2/include LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib -L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm cmake src -DGMX_OPENMM=ON -DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git You have give as an argument to CMake the path the the gromacs/ directory, not the gromacs/src subdirectory! Rossen CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties): set_target_properties called with incorrect number of arguments. -- 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] SwissParam
Thanks for contributing! I added a page about it on the Gromacs website: http://www.gromacs.org/Downloads/Related_Software/SwissParam Rossen On 10/7/10 7:13 PM, Michel Cuendet wrote: SwissParam, a web service that provides topologies and parameters for small organic molecules, compatible with the CHARMM all atoms force field, for use with the CHARMM or GROMACS softwares: http://swissparam.ch/ The server is fully automatic, and the user only needs to provide the organic molecule of interest in the mol2 format. Topology and parameter files are sent back by e-mail, generally within minutes. For GROMACS users, an itp file is generated for the small molecule, which must be included to the protein or DNA topology produced by GROMACS. A tutorial page explains step by step how to set up a protein-ligand system. Force field parameters are derived from the Merck Molecular ForceField (MMFF). Dihedral angle terms are taken as is, while only the harmonic part of the bond, angle and improper terms are retained (the quartic part is discarded). Charges are taken from MMFF. Van der Waals parameters are taken from the closest atom type in CHARMM22. The service is intended for fast and easy force field generation. The parameters have been tested in "drug design" type of calculations, like docking, minimizations, rapid binding energy estimation (LIECE, MMGB/SA), etc... Deeper parameterizations are probably required for applications in which a finer description of the molecule is required, (e.g. normal mode calculations, ...). SwissParam results can then be used as a starting point for such a procedure. Enjoy SwissParam, and please notify us of any question or suggestion for improvement. Try SwissParam now !! -- 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
