[gmx-users] different distance calculated by grompp and g_dist when doing umbrella sampling simulations
Dear All: I encountered a problem when doing umbrella sampling. The distance calculated by grompp and g_dist is different, as shown by the following: grompp z component of g_dist(since I am constraining the distance between two groups along the z direction, I should calculate the z component of the distance, right?) 2.986 2.96 2.953 2.95 2.931 2.92 2.936 2.9355 2.844 2.83 There is an obvious difference between the distance calculated by the grompp and the g_dist, I also found that some post similar problems in the maillist, but I didn't found answers for the following questions. (1)Why there is a such difference? (2)Also, does anyone know which value is used in the umbrella sampling simulations, the grompp result or the g_dist result? (3)how to choose the right starting conformations since there is such a difference? I also pasted the pull code I used as follows: pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes pull_nstxout= 500 pull_nstfout= 500 pull_ngroups= 1 pull_group0 = Protein pull_group1 = AMA pull_init1 = 0 pull_rate1 = 0.000;nm/ps pull_k1 = 4500 ;kJ/mol/nm^2 Thanks in advance!! Best regards, Ruo-Xu Gu -- 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] questiones about dihedral restrain
Dear All: I am using gromacs4.5.3 to do umbrella sampling simulation of the residue side chain dihedrals. I used the dihedral restrain method described in the mannual to restrain the dihedral values. The method we used is described as follows: we first added the following parameters in the *.top file immediately after the parameters of the protein: [ dihedral_restraints ] ; ai ajakal type label phi dphi kfac power 46912 1 1180 0 1 2 Then we added the following parameters in the *.mdp file : ; dihedral restraints dihre = yes dihre_fc= 1000 ; or whatever value you desire dihre_tau = 0.0 nstdihreout = 50 _ Then we used the following commond to generate the tpr file: grompp -f ourfile.mdp -c ourfile.gro -p ourfile.top -o ourfile.tpr After the simulations, we used the g_angle commond to calculate the distribution of the dihedral angels: g_angle_d -f oufile.trr -n ourfile.ndx -od ourfile.xvg -type dihedral However, we found that in the simulation results, the dihedral was not restrained as we expected. The dihedral angles distrbuted in a wide range around its initial values and when larger force constant were applied the distribution was not affected. It seemed that the externial forces we assigned was not applied on the residue. The other parameters we used was the same with that we used in un-restrained simulations. Could anyone help me with this problem? Did I used the wrong parameters or are there any other wrong in my simulations? Thanks in advance. Best Regards r.x.g. -- 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] MD simulations of covalent bound protein-ligand complex by gromacs
Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GROMOS force field. However, I don't know how to made the topology file of the complex, do I need to change the topology file manually to add the necessary things? Thanks in advance! R.X.G. -- 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] sampling the side chain conformations by MD simulations
Dear All: I am conducting molecular dynamics simulations of a proetin. The side chain conformation of one key residue is important for the protein function and I wang to sampling its conformations and calculate the energy barrier when it changes between different conformations. However, the common MD simulations can't sampling all of its conformations (maybe the energy barrier between different conformations is high?) and I want to enhance the sampling process. My question is does it possible to use high temperature for this residue and normal temperature for the other part of the system so that I can sample more conformations in relative short time? I know locally enhanced sampling method maybe useful in this situation, but it seemed that it is not implemented in the GMX package. I will be appraciate if anyone could give me some suggestions. RXG -- 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: some questions about side chain dihedral angle sampling
I forget to say that, there are other residues around that residue whose side chain coformations will affect each others, So, it is difficult to use umbrella sampling method Regards - 原始邮件 - 发件人: mirc...@sjtu.edu.cn 收件人: gmx-users@gromacs.org 发送时间: 星期五, 2012年 3 月 09日 下午 4:58:02 主题: some questions about side chain dihedral angle sampling Dear All: I am doing molecular dynamics simulations of a protein. In my system, there is a critical residue which is important for its activity. I want to sample the side chain conformations of this residue, i.e., calculate the most favourable side chain dihedral angles of this residue and calculate the energy barriers when its side chain conformation changes. Since common MD simulations is too slow to sample all of the possible conformations, my question is does there any methods that can do this kind of sampling quickly in GROMACS? Does Locally Enhanced Molecular Dynamics a proper method? Does there any other possible method? Thanks in advance for all of your helps! Best Regards Ruo-Xu Gu -- 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] some questions about side chain dihedral angle sampling
Dear All: I am doing molecular dynamics simulations of a protein. In my system, there is a critical residue which is important for its activity. I want to sample the side chain conformations of this residue, i.e., calculate the most favourable side chain dihedral angles of this residue and calculate the energy barriers when its side chain conformation changes. Since common MD simulations is too slow to sample all of the possible conformations, my question is does there any methods that can do this kind of sampling quickly in GROMACS? Does Locally Enhanced Molecular Dynamics a proper method? Does there any other possible method? Thanks in advance for all of your helps! Best Regards Ruo-Xu Gu -- 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: problem of installing gromacs4.5.4
Dear Justin: Thank you very much for your reply, but I have another problem. After I install the fftw package, and remove the argument of the --enable-mpi when installing the gromacs package by using the follow commands: export CPPFLAGS=-I/my_path/ export LDFFLAGS=-L/my_path/ ./configure --prefix=my_path --enable-shared --disable-float --enable-mpi make mdrun then I encountered the following errors: libtool: link: cannot find the library `../mdlib/libmd_mpi_d.la' or unhandled argument `../mdlib/libmd_mpi_d.la' make[1]: *** [libgmxpreprocess_mpi_d.la] Error 1 make[1]: directory `/home/dw11-sg007/dying/gromacs-4.5.4/src/kernel' what does this mean? Does it mean there is some problem with the mpi I used? Thanks in advance!! R-X Gu Message: 2 Date: Wed, 04 Jan 2012 09:44:53 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] a installation problem of gromacs4.5.4 using mpi To: Discussion list for GROMACS users Message-ID: <4f0465e5.6090...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed mirc...@sjtu.edu.cn wrote: > Dear All: > > I encountered a problem when installing gromacs4.5.4 by using mpi. When > > I finished the installation successfully, I submit a job by assigning 8 > processes. However, the job was not run by 8 processes, by generate 8 same > jobs each use only 1 process (I have encountered the same problem before, but > it is solved by using the same mpirun path during the installation and the > simulation. However, this time i am sure the path of mpirun assigned during > the installation is the same of that assigned in the simulation command and > this problem occures again.). The followings are the commonds used in my > installation: > > install fftw### > ./configure --prefix=my_path --enable-thread --disable-float --enable-shared > make > make install > > ###install gromacs# > > export CPPFLAGS=-I/my_path/ > export LDFFLAGS=-L/my_path/ > > ./configure --prefix=my_path --enable-shared --disable-float > --enable-mpi=the_path_of_mpirun The --enable-mpi flag does not take any argument. It is also advisable to append a suffix (e.g. _mpi) to the mdrun executable so you can unambiguously use the commands. > make > make install There is no need to try to compile the entire Gromacs package with MPI support; only mdrun is MPI-aware. Instead, use: make mdrun make install-mdrun -Justin > ### > > then I used the following command to do the simulations > > /the_path_of_mpirun/mpirun -np 8 mdrun -s myfile.tpr > > I am sure the path of mpirun assigned during the installation is the same of > that assigned in the simulation command. > > Could anyone tell me how to solve this problem? > > Thanks in advance!! > > R-X Gu > -- 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
[gmx-users] a installation problem of gromacs4.5.4 using mpi
Dear All: I encountered a problem when installing gromacs4.5.4 by using mpi. When I finished the installation successfully, I submit a job by assigning 8 processes. However, the job was not run by 8 processes, by generate 8 same jobs each use only 1 process (I have encountered the same problem before, but it is solved by using the same mpirun path during the installation and the simulation. However, this time i am sure the path of mpirun assigned during the installation is the same of that assigned in the simulation command and this problem occures again.). The followings are the commonds used in my installation: install fftw### ./configure --prefix=my_path --enable-thread --disable-float --enable-shared make make install ###install gromacs# export CPPFLAGS=-I/my_path/ export LDFFLAGS=-L/my_path/ ./configure --prefix=my_path --enable-shared --disable-float --enable-mpi=the_path_of_mpirun make make install ### then I used the following command to do the simulations /the_path_of_mpirun/mpirun -np 8 mdrun -s myfile.tpr I am sure the path of mpirun assigned during the installation is the same of that assigned in the simulation command. Could anyone tell me how to solve this problem? Thanks in advance!! R-X Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] questions about steer molecular dynamics by using gromacs4
Dear All: I am trying to use steer molecular dynamics simulations to pull a ligand along a channel pore (along the Z axis) by constant rate. I know how to realize this by GROMACS3, however, it seemed that in gromacs4, there are some changes regarding this issues, so I am pasting my pull code parameters and some of my questions here, Could any one be so kind to answer my questions? Thanks in advance. My pull code parameters --- pull= umbrella pull_dim= N N Y pull_start = yes ### if the pull_start is set to "yes", it means that, the distance between the pull group and the reference group of the starting structure will be calculated and the value will be added to the pull_init1 and the final result will be used a the inital distance between the pull group and the reference group in the simulations, am i right?### pull_nstxout= 500 ### if the pull_nstxout is set to 500, the COM of the pull group will be write every 500 steps (i.e. 1ps,if the time step is 2fs)? pull_nstfout= 500 pull_group0 = Protein pull_group1 = Ligand pull_vec1 = 0 0 1 pull_init1 = 0 pull_rate1 = 0.025 pull_k1 =1000 how can I make sure the pull_rate1 and the pull_k1 I used is appropriate?###3 __ what is the out put of the pulling code? # Does the above parameters can pull the ligand along the Z axis with a constant rate successfully? Are there any problem the my pull code parameters? Thanks very much for your time and your kind! Best Regards R.-X. Gu -- 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] some problems when using g_membed
Dear All: I am using g_membed command to insert a protein into a membrane bilayer, however, when I run the following command: g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000 I encountered the following errors: Program g_membed, VERSION 4.5.4 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (3270) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Does this mean that there is some un-reasonable physical positions? How can I set the environment variable GMX_MAXCONSTRWARN to -1 or how can I avoid this error? Thanks very much for your time and your kind! Best Regards R.-X. G. -- 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] use AMBER ff03 force field in gromacs 4
Dear All: I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I encountered some problems when generating the topology file of the ligands. I generate the topology file of ligands by using topolbuild package. The atom types of GAFF force field are assigned to the atoms of the ligand. However, when I used grompp command to write the tpr file. There is an error saying: Fatal error: Atomtype c3 not found For more information and tips for troubleshooting, please check the GROMACS It seemed that, the amber ff03 force field in gromacs 4 didn't include the atom types of the GAFF force field. Does any one have ever encountered the same problem? What can I do to solve this problem? this is the topology file of my ligand _- [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB 1 c3 1DRGC12 10.11235 12.00 2 hx 1DRGH13 20.10011 1.00 3 hx 1DRGH14 30.11263 1.00 4 c3 1DRGC15 4 -0.02190 12.00 5 c3 1DRG C4 5 -0.09576 12.00 6 hc 1DRG H5 60.10817 1.00 7 hc 1DRG H6 70.05611 1.00 8 hc 1DRGH16 80.11695 1.00 9 n4 1DRGN10 9 -0.75781 14.00 10 hn 1DRGH11 100.44475 1.00 11 hn 1DRGHN2 110.45369 1.00 12 c3 1DRG C7 120.11240 12.00 13 hx 1DRG H8 130.10008 1.00 14 hx 1DRG H9 140.11262 1.00 15 c3 1DRG C2 15 -0.02192 12.00 16 hc 1DRG H3 160.11695 1.00 17 ca 1DRG C1 17 -0.13377 12.00 18 ca 1DRGC22 18 -0.10700 12.00 19 ha 1DRGH23 190.16944 1.00 20 ca 1DRGC17 20 -0.13377 12.00 21 ca 1DRGC18 21 -0.10699 12.00 22 ha 1DRGH19 220.16945 1.00 23 ca 1DRGC20 230.28871 12.00 24 ca 1DRGC21 240.28875 12.00 25 nb 1DRGN29 25 -0.61584 14.00 26 ca 1DRGC27 260.31853 12.00 27 h4 1DRGH28 270.05520 1.00 28 ca 1DRGC25 280.31854 12.00 29 h4 1DRGH26 290.05519 1.00 30 nb 1DRGN24 30 -0.61586 14.00 [ bonds ] ; aiaj funct r k 2829 1 1.0880e-01 2.8694e+05 2627 1 1.0880e-01 2.8694e+05 2122 1 1.0870e-01 2.8811e+05 1819 1 1.0870e-01 2.8811e+05 1516 1 1.0920e-01 2.8225e+05 1213 1 1.0910e-01 2.8342e+05 1214 1 1.0910e-01 2.8342e+05 910 1 1.0330e-01 3.0878e+05 911 1 1.0330e-01 3.0878e+05 5 6 1 1.0920e-01 2.8225e+05 5 7 1 1.0920e-01 2.8225e+05 4 8 1 1.0920e-01 2.8225e+05 1 2 1 1.0910e-01 2.8342e+05 1 3 1 1.0910e-01 2.8342e+05 2830 1 1.3420e-01 4.0426e+05 2628 1 1.3870e-01 4.0033e+05 2526 1 1.3420e-01 4.0426e+05 2425 1 1.3420e-01 4.0426e+05 2324 1 1.3870e-01 4.0033e+05 2330 1 1.3420e-01 4.0426e+05 2123 1 1.3870e-01 4.0033e+05 2021 1 1.3870e-01 4.0033e+05 1824 1 1.3870e-01 4.0033e+05 1718 1 1.3870e-01 4.0033e+05 1720 1 1.3870e-01 4.0033e+05 1517 1 1.5130e-01 2.7070e+05 1215 1 1.5350e-01 2.5363e+05 912 1 1.4990e-01 2.4568e+05 515 1 1.5350e-01 2.5363e+05 4 5 1 1.5350e-01 2.5363e+05 420 1 1.5130e-01 2.7070e+05 1 4 1 1.5350e-01 2.5363e+05 1 9 1 1.4990e-01 2.4568e+05 [ pairs ] ; aiaj funct 27 29 1 27 30 1 25 29 1 24 27 1 23 29 1 22 24 1 22 30 1 19 20 1 19 23 1 19 25 1 17 22 1 16 18 1 16 20 1 15 19 1 14 16 1 14 17 1 13 16 1 13 17 1 11 13 1 11 14 1 11 15 1 10 13 1 10 14 1 10 15 1
[gmx-users] use AMBER ff03 force field in gromacs 4
Dear All: I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I encountered some problems when generating the topology file of the ligands. I generate the topology file of ligands by using topolbuild package. The atom types of GAFF force field are assigned to the atoms of the ligand. However, when I used grompp command to write the tpr file. There is an error saying: Fatal error: Atomtype c3 not found For more information and tips for troubleshooting, please check the GROMACS It seemed that, the amber ff03 force field in gromacs 4 didn't include the atom types of the GAFF force field. Does any one have ever encountered the same problem? What can I do to solve this problem? Thanks in advance!!! R.X.G. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein
Dear All: I am using GROMACS package to simulate membrane proteins. I plan to use Berger's united atom force field (Berger's UA FF) for lipids and OPLS_AA force field (OPLS_AA FF) for proteins. I have read the guide post kindly by Prof. Dr. Chris Neale in previous mailing lists very carefully. According to his guide, the following steps are needed: 1). Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12 to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected by pope.itp - sigma = (c12/c6)^1/6 - epsilon = c6/(4*sigma^6) 2). Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12 to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all reference to OW to opls_116 (opls spc water oxygen) and simply removed any with reference to HW as it will be zero regardless. 3). Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp. - Prior to running ensure that the non-RB dihedral does not exist for these groups. 4). make a topology file like this: My questions are as follows: 1, Berger's United atom force field scale LJ1-4 interaction by 0.125 and scale Coulombic1-4 interaction by 1.0. OPLS_AA FF scale both of them by 0.5, right? From the above changes, I find that the changes of the sigma or epsilon (or c6 and c12) is only associate with the LJ1-4 interaction. So, how the Coulombic1-4 interaction is scaled properly? Do I need additional changes? 2, the non-bond interactions between the atoms from the lipid and the atoms from the protein are need to be calculated, right? My question is how these interactions are calculated? Does the changes in the [atomtypes]affect these interactions? 3, How the non-bond interactions between the atoms from the lipid are calculated (e.g., the LJ and coulombic interactions)? Does the changes in the [atomtypes]affect these interactions? Thank you very much for your time and your kindness. I really appreciate your help. Regards Ruo-Xu Gu -- 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] topology files for ligands in MD Simulation under OPLS AA force field
Dear All: I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom from the ligands? 2, how to define the charges of each atom? I know that, when the atom type is defined, there will be a corresponding charge to this atom type. Does it safe to use this charge in the simulations on the ligands (since these charges are designed for amino acids)? 3,When the atom type and the charge of atom are defined, how to prepare the file in the GROMACS format? Does there easier method to prepare such files than manually? Thank you very much for your time and your kindness. I really appreciate if any one can share their experience in preparing the topology files for ligands used under OPLS_AA force field and GROMACS package. Sincerely Yours Ruo-Xu Gu -- 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] membrane bilayer simulation by OPLS FF
Dear All: I am using OPLS force field (OPLS FF) to do molecular dynamics simulations. My system contains DPPC lipid, protein and a small molecule. I have the following questions: 1, where can I get the topology files for the DPPC lipids? 2, How to prepare the topology files for the small molecules? I plan to calculate the charges of each atoms by QM method.After I got the charges and atom radius, how to prepare the topology files? 3, I am using GROMACS 3 and I found there are three all-atom force fields there: -- 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges - among them, 6, 7, and 8 are all-atom force fields, right? My question is are 7 and 8 also OPLS force fields? If so, which one is recommendated to use in lipid-protein complex systems MD simulations? What are the differences between 6, 7 and 8. Sincerely Yours Ruo-Xu Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] questions about umbrella sampling
Dear All:
I am using umbrella sampling method to calculate potential of mean
force and I encountered the following questions:
1, at the *.ppa file, I need to incorporate a parameter indicating the
"the position of the pull group will restraint to, relative to the
reference group" (i.e., the "pos1" parameter).
To my understanding, in the initial structure, the pull group is not
need to at the exact position defined by the aformationed parameter
("pos1" parameter) in the .ppa file. I just need to put the pull group
near that position, am I right?
2, Since I need to define the position of the pull group relative to
the reference group. I need to calculate the mass center of the
reference group as well as that of the pull group. Does there any
tools in GROMACS to calculate their mass center?
Thank you very much for your time and your kindness!
Best Regards
R-X Gu
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[gmx-users] questions about umbrella sampling
Dear All:
I am using umbrella sampling method to calculate potential of mean
force and I encountered the following questions:
1, at the *.ppa file, I need to incorporate a parameter indicating the
"the position of the pull group will restraint to, relative to the
reference group" (i.e., the "pos1" parameter).
To my understanding, in the initial structure, the pull group is not
need to at the exact position defined by the aformationed parameter
("pos1" parameter) in the .ppa file. I just need to put the pull group
near that position, am I right?
2, Since I need to define the position of the pull group relative to
the reference group. I need to calculate the mass center of the
reference group as well as that of the pull group. Does there any
tools in GROMACS to calculate their mass center?
Thank you very much for your time and your kindness!
Best Regards
R-X Gu
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[gmx-users] problems when using command "trjconv"
Dear All: I encounter some problems when I am using command "trjconv" to remove the periodic boundary condition. I am doing molecular dynamics simulations of a pentamer, and some of the subunits "jump" from one box to its adjacent one. Thus, I try to remove the periodic boundary conditions by trjconv command.The commands I used are as follows: trjconv -s trpfile -f xtcfile -o new_xtcfile -n index.ndx -pbc nojump In the results I found the five subunits are put together to form the initial pentamer which is what I expected. However, I also found some of the subunits are cut off a part (i.e., the subunit is broken into one large piece and several small pieces, the large piece forms pentamer with other subunits, and the small pieces distribute in the boundary of the box). Then, I try to solve this problem by using the follow command: trjconv -s trpfile -f new_xtcfile_lastCommand -o another_new_xtcfile -n index.ndx -pbc whole this time, the subunits are not broken, but the pentamer is not formed(i.e., some subunits in one box and some in the adjancent one). Thus, I am writing to find a way in order to remove the periodic boundary condition and put the subunits together as a pentamer with out break a seperate subunit into several parts.Could anyone be so kind to give me some suggestions? Thank you very much for your insight. Best Wishes R-X Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] some questions about umbrella sampling
Dear All: I am doing umbrella sampling to calculate energy profile of an drug passing through a ion channel by GROMACS3.3. In order to get right result, I need to choose a reasonable force constant in my simulation, right? I know that, a reasonable force constant should produce enough "overlap" to reduce WHAM errors, But I'm wondering "how much overlap" are reasonable overlap?Does there any rules I can use to judge whether my "overlap" is enough? My second question is that, how to choose "number of bins", when I using g_wham command? Does it decided by the numbers of windows I used? I found that, different numbers will produce slightly different results (a difference of 0.5kcal/mol in my condition). What does it mean? Does it mean that, my simulation is not enough? the third question: I found someone say that, to get results in a good quality, one must make sure that, "individual histograms should look smooth". What does it mean? Does it mean that,the distribution of the positions of the drug in one window should be "smooth" or should opproximately be an Gauss distribution(I found that, whether it is smooth is decided by the number of bins, if a very large number of bins is used, it is not smooth)? The last question: if my simulation produced enough "overlap", can I believe that, my simulation is "right" theoretically? Thanks in advance!!! R-X Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force constant for umbrella sampling potential
Hello everyone, I would like to know does the harmonic biasing potential for running umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term incorporated into the force constant value that we specify? On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2. I am using Grossfield�s WHAM algorithm and it assumes that the biasing potential used has a 0.5 in front, but I know for example CHARMM does not include the 0.5 and I just need to know if this is also the case with gromacs Thank you in advance. R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_wham error
Dear All: I did some umbrella sampling and got series of .pdo files. I want to calculate potential of mean force (PMF) by g_wham command. However I encount some problems: when I input the following command: g_wham pull.pdo -o xx.xvg -hist xx2.xvg -temp 300 the programme give me the following errors: :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_wham (-: Option Filename Type Description -o xx.xvg Output xvgr/xmgr file -hist xx2.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -min real 0 Minimum coordinate in profile -max real 0 Maximum coordinate in profile -binsint100 Number of bins in profile -[no]profbool yes Only calculate min and max -tempreal 300 Temperature -[no]flipbool no Combine halves of profile -tol real 0.01Tolerance Opening file pull.pdo. gunzip: stdin: not in gzip format --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 89 Fatal error: This does not appear to be a valid pdo file --- Since it remained me that pull.pdo is not in gzip format, i compress the fill by gzip command of linux system, and got pull.pdo.gz file, then i input g_wham pull.pdo.gz -o xx.xvg -hist xx2.xvg -temp 300 it still give me the following errors: :-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_wham (-: Option Filename Type Description -o xx.xvg Output xvgr/xmgr file -hist xx2.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -min real 0 Minimum coordinate in profile -max real 0 Maximum coordinate in profile -binsint100 Number of bins in profile -[no]profbool yes Only calculate min and max -tempreal 300 Temperature -[no]flipbool no Combine halves of profile -tol real 0.01Tolerance Opening file pull.pdo.gz. --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 89 Fatal error: This does not appear to be a valid pdo file --- Since it remaind me that, "This does not appear to be a valid pdo file", so does my .pdo file has some errors? I past the head of the .pdo file in the following: # UMBRELLA 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group '' # Nr. of pull groups
[gmx-users] about free energy calculation by LIE method
Dear All: I want do some free energy calculation by LIE method. I read the "GROMACS Tutorial for Drug ? Enzyme Complex" carefully and know the method in gromacs to do free energy calculatin by LIE method. However I found the following words at the end of the tutorial: "In this tutorial, we used PME and full periodic boundary conditions. Performing LIE computations with PME requires additional work to account for the longrange contribution. This takes a lot of work! We recommend using NVT ensemble using a water shell with cutoffs or Shift." Does anyone can tell me what additional work do I need to do if I want to calculate free energy by LIE method when I used PME in my simulation. Or, dose anyone know how to using a water shell in gromacs simulation, inorder to do free energy calculation by LIE method in a right way? Thank you in advance. R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about PMF calculation
Dear All: I want to do some PMF (Potenial of Mean Force) calculation by AFM pulling method using the pull code to study the unbinding of a protein and a ligand. I want pull the ligand from its binding site and calculate the PMF of the procedure, does it possible? I have read the user manual about PMF calculation carefully, but still not clear how to do . Does anyone have any tutorial about how to do this kind of calculation or any published papers doing this things? anyhelp is greatly appreciate! Best Wishes R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about coorelation fluctuation calculation
Dear all: I finished a MD simulation and i want to calculation the correlation fluctuation of the alpha C.Does there any tools that can do this in gromacs package (I have tried g_rmsf -oc , but it doesn't work,specificly, the -oc command give no result) ? Can any one be so kind to help me out?Thanks very much. R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] estimate the binding free energy. long range electrostatic interaction
> mirc...@sjtu.edu.cn wrote: >> Dear All: >> >> I would like to estimate the binding free energy between a drug >> molecule and its receptor. Inorder to do this, i run a MD simulation in >> which PME method was used to deal with long range electrostatic >> interaction. >> I need to calculate the VDW interaction energy and electorstatic >> interaction energy between the drug and its enviornment to calculate the >> free energy(I cannot use the g_lie tool since I know I have to mind the >> PME contribution). >> >> For VDW interaction energy, i calculate the >> LJ-SR(drug-enviornment) and LJ-LR(drug-enviorment), so the VDW >> interaction energy is the sum of them.However, I got PROBLEM when i try >> to calculte the electrostatic interaction energy: if i use g_energy to >> read energy form .edr file, there is onley Coul-SR, but I also need the >> Coul_LR to calculate the electrostatic interaction energy.By checking >> the previous questiones and answers, I know that Coul.-recip.is the >> contirbution of PME. But, the "Coul.-recip" read form .edr file by >> g_energy is not the long range electrostatic interaction energy between >> the drug and enviorment, it seems to contain other thing. How can i get >> the long range electorstatic interaction between the drug and the >> enviornment? > > True, Coul.-recip has other components in there. There's no way to > decompose it. However the quantity in which you are actually interested > is the difference between the long-range electrostatic interaction > energy of two states, which in the limit of infinite sampling converges > to the difference between Coul.-recip values. Presumably this issue has > been dealt with in the literature, so look for recent published > methodologies using the LIE method. > > Mark Dear Mark: I read some materials talking about this issue,it is said =20 that,i should rerun my trajectury with the charges of my ligand set to zero, and calculate the =20 "Coul.-recip" again.Subtract this value from the previous "Coul.-recip." and the result is the long range =20 electrostatic interaction energy between the ligand and its enviornment. Is this method right? R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about estiminating the binding free energy by LIE method
Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and electorstatic interaction energy between the drug and its enviornment to calculate the free energy(I cannot use the g_lie tool since I know I have to mind the PME contribution). For VDW interaction energy, i calculate the LJ-SR(drug-enviornment) and LJ-LR(drug-enviorment), so the VDW interaction energy is the sum of them.However, I got PROBLEM when i try to calculte the electrostatic interaction energy: if i use g_energy to read energy form .edr file, there is onley Coul-SR, but I also need the Coul_LR to calculate the electrostatic interaction energy.By checking the previous questiones and answers, I know that Coul.-recip.is the contirbution of PME. But, the "Coul.-recip" read form .edr file by g_energy is not the long range electrostatic interaction energy between the drug and enviorment, it seems to contain other thing. How can i get the long range electorstatic interaction between the drug and the enviornment? Does any one can be so kind to give me some advise? Thank you very much. Best Regards R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] estimate free energy bu LIE method, about long range electrostatic interaction
Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and electorstatic interaction energy between the drug and its enviornment to calculate the free energy(I cannot use the g_lie tool since I know I have to mind the PME contribution). For VDW interaction energy, i calculate the LJ-SR(drug-enviornment) and LJ-LR(drug-enviorment), so the VDW interaction energy is the sum of them.However, I got PROBLEM when i try to calculte the electrostatic interaction energy: if i use g_energy to read energy form .edr file, there is onley Coul-SR, but I also need the Coul_LR to calculate the electrostatic interaction energy.By checking the previous questiones and answers, I know that Coul.-recip.is the contirbution of PME. But, the "Coul.-recip" read form .edr file by g_energy is not the long range electrostatic interaction energy between the drug and enviorment, it seems to contain other thing. How can i get the long range electorstatic interaction between the drug and the enviornment? Does any one can be so kind to give me some advise? Thank you very much. Best Regards R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
