[gmx-users] question in pulling in gromacs 4.0
Hi , I want to pull a molecule from the membrane. My complete mdp file is the following ;. ; File 'mdout.mdp' was generated ; By user: psn (17109) ; On host: p690k ; At date: Fri Jul 23 12:43:31 2004 ; ; VARIOUS PREPROCESSING OPTIONS = title= lipid bilayer in water cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 500 dt = 0.002 nsteps = 175 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ;bd-temp = 300 ;I have commute the above line as it has no exitance bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 250 nstenergy= 250 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME ;Reaction-Field rcoulomb-switch = 0 rcoulomb = 1.0 ;2.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 80.0 epsilon_rf = 1 ;I have done some thing new according to mannual and warnings and error ; Method for doing Van der Waals = vdwtype = Cut-off ; cut-off lengths= rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = berendsen ; Groups to couple separately = tc-grps = DPP SOL Na PIP ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 0.1 0.1 0.1 ref_t= 310 310 310 310 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.01.0 ; SIMULATED ANNEALING CONTROL = annealing= no ; Time at which temperature should be zero (ps) = ;zero-temp_time = 0 ;I have commute the above line as it has no exitance ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 310.0 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = all-bonds ; Type of constraint algorithm = constraint_algorithm = lincs ; Do not constrain the start configuration = unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations = Shake-SOR= no ; Relative tolerance of shake = shake-tol
Re: [gmx-users] question in pulling in gromacs 4.0
anirban polley wrote: Hi , I want to pull a molecule from the membrane. My complete mdp file snip ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 310.0 gen_seed = 173529 Equilibrate first, then do funky things. Here, in the first step, there is no error or warning during the making of .tpr file.But in the mdrun, after 3/4 steps, it crashes ans stop the MD run. It gives the following error message: Back Off! I just backed up dppc_pip2-ion_NPT_berendsen_md.edr to ./#dppc_pip2-ion_NPT_berendsen_md.edr.2# starting mdrun 'Pure 122 DPPC and 1 PIP2 molecule bilayer with 3592 water molecules' 175 steps, 3500.0 ps. step 0 Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511 Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511 Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511 . t = 500.004 ps: Water molecule starting at atom 10595 can not be settled. Check for bad contacts and/or reduce the timestep. Step 2, time 500.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 35.655980, max 638.714233 (between atoms 2849 and 2848) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 943942 54.90.1498 3.0441 0.1530 942941 88.60.1297 0.2327 0.1530 943944 93.10.1291 20.4158 0.1530 944945 93.60.1491 116.4443 0.1530 Wrote pdb files with previous and current coordinates - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 21625 failed on node n0 (127.0.0.1) due to signal 11. - http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25 Mark ___ 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
Re: [gmx-users] question in pulling in gromacs 4.0
anirban polley wrote: ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = berendsen ; Groups to couple separately = tc-grps = DPP SOL Na PIP ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 0.1 0.1 0.1 ref_t= 310 310 310 310 In addition to Marks' advice, don't couple solvent and ions separately. This is a common error. See here: http://wiki.gromacs.org/index.php/Thermostats -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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
Re: [gmx-users] How to calculate PMF after AFM pulling
huifang liu wrote: Hi Justin, Thank you for your reply, but i am still a little confused. You said in principal I should be able to extract a potential of mean force from an AFM run by simply integrating the average force along the reaction coordinate and if I have the average force as a function of position, I could simply integrate that to get the PMF. However, actually, i don't I didn't say that. The post I pointed you to did :) know how i can get the average force as a function of position and apply them in the PMF calculation. Could you give me some suggestion? Your .pdo file should have the forces, if I remember the old (3.3.x, right?) file format correctly. Then something like g_traj can extract coordinates from your trajectory. Also a good reference (and there is a ton of stuff in the list archive about this, hint): http://www.gromacs.org/pipermail/gmx-users/2002-August/002241.html I've not tried to do PMF analysis this way. It is much easier under 4.0 now to use umbrella sampling since g_wham now works. It was non-functional (or buggy at best) in previous versions. -Justin Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com mailto:huifangliu1...@gmail.com Fax: (86-21)54237264 ___ 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 -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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] localp
Hi Guys, May anyone tell me how to calculate the local pressure in a lipid bilayer using Gromacs? In this context, I knew about the existence of g_localp, but it is missed in the new versions of Gromacs. In addition, is it possible to extract the force tensor Fij for all the atom pairs of a certain system from the simulated trajectory? Thank you very much in advance for your assistance, Javier -- Dr. Jose Javier Lopez Cascales Profesor Titular de Universidad Grupo de Bioinformatica y Macromoleculas (BioMac) Area de Quimica Fisica Universidad Politecnica de Cartagena Campus de Alfonso XIII, Aulario II 30203 Cartagena, Murcia Spain Phone: +34-968-325567 Fax..: +34-968-325931 Skype: jjlopezcascales e-mail...: javier.lo...@upct.es website: http://www.upct.es/~biomac/javier.html ___ 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] [Fwd: Problems in pulling a molecule from the membrane]
I have tested the pulling in GROMACS 4.0.2 only once and there only with 'pull_geometry = position'. But i think the problem lies in the pressure-coupling or something which is connected to it ' Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511'. Because i have not yet used pressure-coupling (only done NVT) . So the only think i can do is: Look at: http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25 Sorry that i can not give more help. Probably one thing: I would try 'tinit=0'. I do not know how the code works, but i can imagine that with a non-zero value, the spring move but the system cannot do something. Then when the real simulation begins the spring has actually moved and you have an force acting on your pull-group which is much higher then with 'tinit=0'. But this is only an idea and i do not know if it has any relevance . Probalby one of the other guys knows if this matters. Thomas Dear Thomas, I found your name from the gromacs mailing list. As you are the one of the fortunate persons who has able to do pulling in gromacs 4.02, I directly mail you. I want to pull a molecule from the membrane. My complete mdp file is the following ;. ; File 'mdout.mdp' was generated ; By user: psn (17109) ; On host: p690k ; At date: Fri Jul 23 12:43:31 2004 ; ; VARIOUS PREPROCESSING OPTIONS = title= lipid bilayer in water cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 500 dt = 0.002 nsteps = 175 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ;bd-temp = 300 ;I have commute the above line as it has no exitance bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 250 nstenergy= 250 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME ;Reaction-Field rcoulomb-switch = 0 rcoulomb = 1.0 ;2.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 80.0 epsilon_rf = 1 ;I have done some thing new according to mannual and warnings and error ; Method for doing Van der Waals = vdwtype = Cut-off ; cut-off lengths= rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = berendsen ; Groups to couple separately =
RE: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]
Hi, First let me say you should change to 4.0.4. I don't recall if there would be problems with your setup, but 4.0.4 has many bugfixes. I guess you problem is that you use pull_start and pull_init togther, which I guess produces double the effect you want. Please read the mdp manual. I guess you should use only one of the two options. Berk Date: Fri, 27 Mar 2009 14:43:48 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane] I have tested the pulling in GROMACS 4.0.2 only once and there only with 'pull_geometry = position'. But i think the problem lies in the pressure-coupling or something which is connected to it ' Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511'. Because i have not yet used pressure-coupling (only done NVT) . So the only think i can do is: Look at: http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25 Sorry that i can not give more help. Probably one thing: I would try 'tinit=0'. I do not know how the code works, but i can imagine that with a non-zero value, the spring move but the system cannot do something. Then when the real simulation begins the spring has actually moved and you have an force acting on your pull-group which is much higher then with 'tinit=0'. But this is only an idea and i do not know if it has any relevance . Probalby one of the other guys knows if this matters. Thomas Dear Thomas, I found your name from the gromacs mailing list. As you are the one of the fortunate persons who has able to do pulling in gromacs 4.02, I directly mail you. I want to pull a molecule from the membrane. My complete mdp file is the following ;. ; File 'mdout.mdp' was generated ; By user: psn (17109) ; On host: p690k ; At date: Fri Jul 23 12:43:31 2004 ; ; VARIOUS PREPROCESSING OPTIONS = title= lipid bilayer in water cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 500 dt = 0.002 nsteps = 175 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ;bd-temp = 300 ;I have commute the above line as it has no exitance bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 250 nstenergy= 250 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME ;Reaction-Field rcoulomb-switch = 0 rcoulomb = 1.0 ;2.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 80.0 epsilon_rf = 1 ;I have done some thing new according to mannual and warnings and error ; Method for doing Van der Waals = vdwtype = Cut-off ; cut-off lengths= rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the
[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that I find would help me to make my ideas more clear: 1-am I overestimating the importance of ligand charges in such a simple study of protein-small molecule (containg charged Phosphate groups) complex? or 1.1-The only way to test for this is doing many different simulation on the same system using different type of computed charges to see what happen? 2-How could I try to choose a method to obtain reasonable charges based on the reproduction of experimentally-observed behavior if I do not have experimental data for my system? 3-I also would like to know from users dealing with protein-ligand interactions studies what do you consider a good approach to address this problem? Based on what I read I'd have a tendency to use HF/6-31G** ESP derived charges (with necessary changes as to make it united-atom charges and scaling that to a integer number for each group). Please, let me know if that strategy would be as good as a disaster! Thank you very much for the attention. Josmar Rocha Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ 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
Re: [gmx-users] How to add another electrostatic summation methodin Gromacs
Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot use the user defined part to do my eletrostatic summation. I compared carefully with Wolf summation with the Ewald summation, the differences are: 1. There is no reciprocal term in Wolf. 2.Instead, the Wolf assums that the ions out side the truncations sphere is exactly located at the sphere. That is how the extra two terms come out. 3. Wolf uses cut-off, while Ewald can only deal with peoriodical boundary conditions cases. So I need to add a similiar summation like Ewald to treat with the long-range electrostatic force, not a non-bonded interaction. Then which parts needs to be read and modified? Thank you for your kindly help. Shuangxing Dai - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 26 March, 2009 4:56 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodin Gromacs Shuangxing Dai wrote: Thank you for your help. I attached the page of the form of potential. The equation (5.13) gives all the potential energy of neighbours of one ion in a truncation sphere. Rc is cut-off. Since this potential depends on all the neighbours in a cut-off distance, I cannot give the pair interaction because in this method, only the total potential energy of one ion maks sense. In Ewald summation, both the real space and reciprocal space summation can be written as the summation of pair potential. But in wolf, I cannot do that. It looks separable into a double sum over atom pairs from within a cutoff, since the value of that limit is constant. Since I cannot use Ewald without peoriodical boundary conditions while this Wolf method can, so I cannot simply use Gromacs to do my simulation. The question is which files needed to be modified if I want to add a new one? Is there any direct way? Or I should read all the whole code? You can start by reading the kernel code generated by mknb during the make process and found in src/gmxlib/nonbonded/nb_kernel. If you play with the flags to mknb you can get comments embedded in the C files. Find the one that does Ewald without table lookups and consider how you'd need to change it to suit your needs. Mark ___ 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 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
Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that I find would help me to make my ideas more clear: 1-am I overestimating the importance of ligand charges in such a simple study of protein-small molecule (containg charged Phosphate groups) complex? or 1.1-The only way to test for this is doing many different simulation on the same system using different type of computed charges to see what happen? 2-How could I try to choose a method to obtain reasonable charges based on the reproduction of experimentally-observed behavior if I do not have experimental data for my system? 3-I also would like to know from users dealing with protein-ligand interactions studies what do you consider a good approach to address this problem? Based on what I read I'd have a tendency to use HF/6-31G** ESP derived charges (with necessary changes as to make it united-atom charges and scaling that to a integer number for each group). Please, let me know if that strategy would be as good as a disaster! Thank you very much for the attention. Josmar Rocha Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com ___ 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
Re: [gmx-users] How to add another electrostatic summation methodin Gromacs
Shuangxing Dai wrote: Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot use the user defined part to do my eletrostatic summation. If N is the number of neighbours inside the cutoff distance, then you might be right. If so, then I don't understand why the inner summation constrains j != i and r_ij R_c since the latter is implied by formation of the set over which the summations are occurring. If N is the total number of ions then the last few terms are all system-wide constants. I also don't understand why the limit expression exists. For any values actually used in a simulation, that expression is just a constant. I compared carefully with Wolf summation with the Ewald summation, the differences are: 1. There is no reciprocal term in Wolf. 2.Instead, the Wolf assums that the ions out side the truncations sphere is exactly located at the sphere. That is how the extra two terms come out. 3. Wolf uses cut-off, while Ewald can only deal with peoriodical boundary conditions cases. So I need to add a similiar summation like Ewald to treat with the long-range electrostatic force, not a non-bonded interaction. Then which parts needs to be read and modified? I don't understand your conclusion, here. Mark ___ 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
Re: [gmx-users] How to add another electrostatic summation methodinGromacs
- Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 27 March, 2009 5:01 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodinGromacs Shuangxing Dai wrote: Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot use the user defined part to do my eletrostatic summation. If N is the number of neighbours inside the cutoff distance, then you might be right. If so, then I don't understand why the inner summation constrains j != i and r_ij R_c since the latter is implied by formation of the set over which the summations are occurring. If N is the total number of ions then the last few terms are all system-wide constants. Sorry, (5.13) is the total electrostatic potential energy for the system and the N is the total number of ions. I also don't understand why the limit expression exists. For any values actually used in a simulation, that expression is just a constant. In simulation, we simply uses r_ij = R_c, so ignore the limit. I compared carefully with Wolf summation with the Ewald summation, the differences are: 1. There is no reciprocal term in Wolf. 2.Instead, the Wolf assums that the ions out side the truncations sphere is exactly located at the sphere. That is how the extra two terms come out. The second and third terms came from this treatment. 3. Wolf uses cut-off, while Ewald can only deal with peoriodical boundary conditions cases. So I need to add a similiar summation like Ewald to treat with the long-range electrostatic force, not a non-bonded interaction. Then which parts needs to be read and modified? I don't understand your conclusion, here. OK. I mean I need to add a eletrostatic summation method very similiar to Ewald. So where is definition/algorithm of Ewald in Gromacs and how to add one? Thank you for your kind help. Mark ___ 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 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
Re: [gmx-users] How to add another electrostatic summation methodinGromacs
Shuangxing Dai wrote: - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 27 March, 2009 5:01 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodinGromacs Shuangxing Dai wrote: Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot use the user defined part to do my eletrostatic summation. If N is the number of neighbours inside the cutoff distance, then you might be right. If so, then I don't understand why the inner summation constrains j != i and r_ij R_c since the latter is implied by formation of the set over which the summations are occurring. If N is the total number of ions then the last few terms are all system-wide constants. Sorry, (5.13) is the total electrostatic potential energy for the system and the N is the total number of ions. So the total number of neighbours in a cut off distance doesn't seem to enter the expression... I also don't understand why the limit expression exists. For any values actually used in a simulation, that expression is just a constant. In simulation, we simply uses r_ij = R_c, so ignore the limit. Sure I compared carefully with Wolf summation with the Ewald summation, the differences are: 1. There is no reciprocal term in Wolf. 2.Instead, the Wolf assums that the ions out side the truncations sphere is exactly located at the sphere. That is how the extra two terms come out. The second and third terms came from this treatment. 3. Wolf uses cut-off, while Ewald can only deal with peoriodical boundary conditions cases. So I need to add a similiar summation like Ewald to treat with the long-range electrostatic force, not a non-bonded interaction. Then which parts needs to be read and modified? I don't understand your conclusion, here. OK. I mean I need to add a eletrostatic summation method very similiar to Ewald. So where is definition/algorithm of Ewald in Gromacs and how to add one? Such a summation method is algorithmically a short-range interaction, not a long-range one (like a reaction-field contribution, or a mesh contribution from PME or PPPM), which is the reason I didn't understand your conclusion above. Like I said a day or two back, the nonbonded kernels do the real-space summation for Ewald. For speed, in the optimized kernels the erfc(alpha*r)/r bit is pre-computed in a table and looked up. Hence wanting to cast your expression to use the same trick. Mark ___ 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
