Re: [gmx-users] how to make topol.top file for mixed solution
cuong nguyen wrote: Dear, Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system. So please help me to create a suitable topol.top file to this system. No one can help you without knowing the exact errors that grompp produced. -Justin Thanks a lot. Best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Justin A. Lemkul wrote: cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please read the tutorial: http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems Also possibly useful: http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] refcoord_scaling
On 7/11/2011 4:53 PM, khuchtumur bumerdene wrote: Hi, I have a question about refcoord_scaling option and its role in pressure coupling. What I'm currently doing is just running the lysozyme tutorial on my own protein. I've so far had successful runs when equilibrating on my own machine, which is currently running gmx4.5.3. NPT came to a stable average of ~1.0 bar. But when I do it on the cluster with gmx4.5.5, grompp gives the following error: WARNING 1 [file npt.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. That's a warning, not an error. You need to apply judgement about whether a warning is significant. Possibly this warning was introduced between 4.5.3 and 4.5.5. If so, then the reason for the warning message still applied to the 4.5.3 run and ignorance was bliss :-) My npt.mdp file is as follows (straight from the tutorial at this stage): define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 15 ; 2 * 15 = 300 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off The only change I made is the nsteps as my box is bigger and thus has more waters in it. So after reading the warning I tried to find some info on the refcoord_scaling, which the only information found by my feeble attempts were from the mdp options and the manual, which states: *refcoord_scaling:* *no* The reference coordinates for position restraints are not modified. Note that with this option the virial and pressure will depend on the absolute positions of the reference coordinates. *all* The reference coordinates are scaled with the scaling matrix of the pressure coupling. *com* Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account. I don't quite understand this completely, is the option there to change the coordinates of the solute as the box size changes, where the 'all' option changes the coordinates of every atom and the com only changes the coordinates of the solute com? Please correct me on this. Under NPT the box size changes each step. You are using position restraints to a pre-defined set of reference coordinates. This option allows you to choose how those *reference coordinates* should change when the box size changes (respectively do not scale them at all, scale them all, or scale their COM
[gmx-users] orca and qm/mm
Dear all users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse = no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! thank you! -- 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] orca and qm/mm
All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse = no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- 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] orca and qm/mm
Try not leaving QMmethod andQMbasis entries empty even if these data are read from orca input (in BASENAME.ORCAINFO). You can check in the input files (.inp) generated by GROMACS the actual commands used by ORCA. El 07/11/11 13:54, xi zhao escribió: All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFOfile: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator= md tinit= 0 dt= 0.001 nsteps= 500 nstcomm= 1 comm_grps= system emtol= 100.0 emstep= 0.001 nstcgsteep= 50 nstxout= 1 nstvout= 1 nstfout= 1 nstlog= 1 nstenergy= 1 nstxtcout= 1 xtc_grps= system energygrps= QMatoms rest_Protein SOL nstlist= 10 ns_type= grid pbc= xyz rlist= 1.0 coulombtype= cut-off rcoulomb = 1.4 epsilon_r= 1 vdwtype= Cut-off rvdw= 1.4 tcoupl= berendsen tc-grps= rest_Protein SOL QMatoms tau_t= 0.1 0.1 0 ; QM atoms are uncoupled ref_t= 300 300 300 Pcoupl= Berendsen pcoupltype= isotropic tau_p= 1.0 compressibility= 4.5e-5 ref_p= 1.0 free_energy= no init_lambda= 0 delta_lambda= 0 QMMM= yes QMMM-grps= QMatoms QMmethod= QMbasis= QMMMscheme= normal QMcharge= -1 CASelectrons= CASorbitals= SH= gen_vel= no gen_temp= 300 gen_seed= 173529 constraints= all-bonds constraint_algorithm= LINCS unconstrained_start= yes shake_tol= 0.0001 lincs_order= 4 lincs_warnangle= 30 morse= no According to the instruction In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored)., the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr .. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- 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] umbrella sampling with pull=constraint
Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance between the reference and pulling group. Can we use pull=constraint option to retain the pulling group within the COM distance? my pulling code is as bellow with restrain at 0.5nm distance from ref group. I just want to get some idea about this pull code modification. pull= constraint pull_geometry= distance pull_dim= N N Y pull_start = no pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = Chain_B pull_init1 = 0.50 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 500 pull_nstfout= 500 Regards, Vijay. -- 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] orca and qm/mm
Just put something in QMMMscheme etc.. This will subsequently be overwritten by whatever you have in your ORCA file. Micha On 07/11/11 12:54, xi zhao wrote: All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFOfile: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator= md tinit= 0 dt= 0.001 nsteps= 500 nstcomm= 1 comm_grps= system emtol= 100.0 emstep= 0.001 nstcgsteep= 50 nstxout= 1 nstvout= 1 nstfout= 1 nstlog= 1 nstenergy= 1 nstxtcout= 1 xtc_grps= system energygrps= QMatoms rest_Protein SOL nstlist= 10 ns_type= grid pbc= xyz rlist= 1.0 coulombtype= cut-off rcoulomb = 1.4 epsilon_r= 1 vdwtype= Cut-off rvdw= 1.4 tcoupl= berendsen tc-grps= rest_Protein SOL QMatoms tau_t= 0.1 0.1 0 ; QM atoms are uncoupled ref_t= 300 300 300 Pcoupl= Berendsen pcoupltype= isotropic tau_p= 1.0 compressibility= 4.5e-5 ref_p= 1.0 free_energy= no init_lambda= 0 delta_lambda= 0 QMMM= yes QMMM-grps= QMatoms QMmethod= QMbasis= QMMMscheme= normal QMcharge= -1 CASelectrons= CASorbitals= SH= gen_vel= no gen_temp= 300 gen_seed= 173529 constraints= all-bonds constraint_algorithm= LINCS unconstrained_start= yes shake_tol= 0.0001 lincs_order= 4 lincs_warnangle= 30 morse= no According to the instruction In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored)., the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr .. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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 1. orca and qm/mm (xi zhao)
Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error. Gerrit On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. orca and qm/mm (xi zhao) -- Message: 1 Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST) From: xi zhao zhaoxiitc2...@yahoo.com.cn Subject: [gmx-users] orca and qm/mm To: gmx-users@gromacs.org Message-ID: 1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com Content-Type: text/plain; charset=utf-8 All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit= 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps= system emtol= 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy= 1 nstxtcout= 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r= 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t= 0.1 0.1 0 ; QM atoms are uncoupled ref_t= 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps= QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol= 0.0001 lincs_order = 4 lincs_warnangle = 30 morse= no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2007/8c5c63c5/attachment-0004.html -- -- 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! End of gmx-users Digest, Vol 91, Issue 36 * -- 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] umbrella sampling with pull=constraint
Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list. Nevertheless, you do need to worry about which images are used to derive the pulling forces. You can often do that by a judicious selection of pull_pbcatom (read about that on-list and in the manual). In some cases, however, pull_pbcatom can not assist enough and you are forced to make the box larger. None of this is alleviated by pull=constraint, which is why I'm not going to answer your question about your .mdp parameters at this point. Let's get the problems identified and solved first with pull=umbrella. Chris. -- original message -- Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance between the reference and pulling group. Can we use pull=constraint option to retain the pulling group within the COM distance? my pulling code is as bellow with restrain at 0.5nm distance from ref group. I just want to get some idea about this pull code modification. pull= constraint pull_geometry= distance pull_dim= N N Y pull_start = no pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = Chain_B pull_init1 = 0.50 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 500 pull_nstfout= 500 Regards, Vijay. -- 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] PBC - Protein - ligand
Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Steven -- 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:umbrella sampling with pull=constraint
If you use constraints it would not be umbrella sampling, where you need to sample around a restraint structure to get the histograms for WHAM or another analysis-technic. So if you want to do umbrella sampling either make to box bigger and/or make the restraints harder. But you can also use constraints instead of restraints. But it would require another analysis-technic. Think it's called thermodynamic integration. In the end you also sample many different windows with varying distances, but instead of using WHAM you integrate the constraint force to obtain the PMF. http://www.sciencedirect.com/science/article/pii/000926149190259C One important thing to note is, that you will need more windows compared to umbrella-sampling, since in each window you sample only on distance and not around one distance (restrains allow for a change of the distance). Another thing to note is the pull_dim. For determining the PMF of an end-toend distance of similar i would turn all three dimensions to 'yes'. Imagine to parallel sheets of paper, with z perpendicular to the papers. With your setup you would only fix the z-distance between both sheets, but they can move freely in the xy-plane. Hope that helps. greetings thomas Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance between the reference and pulling group. Can we use pull=constraint option to retain the pulling group within the COM distance? my pulling code is as bellow with restrain at 0.5nm distance from ref group. I just want to get some idea about this pull code modification. pull= constraint pull_geometry= distance pull_dim= N N Y pull_start = no pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = Chain_B pull_init1 = 0.50 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 500 pull_nstfout= 500 Regards, Vijay. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein - ligand
Hi Steven, Don't use -ur compact in the first step and see if that solves the problem. Oh, and be sure that the thing is not just diffusing. There was a thread lately where a diffusing ligand drove someone mad trying to remove the 'jumps'. Cheers, Tsjerk On Mon, Nov 7, 2011 at 3:08 PM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Steven -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein - ligand
Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Center on either the protein, the ligand, or some custom index group of residues surrounding the ligand. Centering on the whole system usually doesn't do anything useful. -Justin Steven -- 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
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
= no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2007/8c5c63c5/attachment-0004.html -- -- 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! End of gmx-users Digest, Vol 91, Issue 36 * -- 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
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
in addition, how to write ORCAINFO? Is my file right? ! RKS B3LYP/G SV(P) TightSCF Opt or RKS B3LYP/G SV(P) TightSCF Opt --- 11年11月7日，周一, Gerrit Groenhof ggro...@gwdg.de 写道： 发件人: Gerrit Groenhof ggro...@gwdg.de 主题: [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午9:23 Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error. Gerrit On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. orca and qm/mm (xi zhao) -- Message: 1 Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST) From: xi zhao zhaoxiitc2...@yahoo.com.cn Subject: [gmx-users] orca and qm/mm To: gmx-users@gromacs.org Message-ID: 1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com Content-Type: text/plain; charset=utf-8 All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse = no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2007/8c5c63c5/attachment-0004.html -- -- 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! End of gmx-users Digest, Vol 91, Issue 36 * -- 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
Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
epsilon_r= 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t= 0.1 0.1 0 ; QM atoms are uncoupled ref_t= 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps= QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol= 0.0001 lincs_order = 4 lincs_warnangle = 30 morse= no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2007/8c5c63c5/attachment-0004.html -- -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=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! End of gmx-users Digest, Vol 91, Issue 36 * -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?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] Re: umbrella sampling with pull=constraint
Hello, Thanks for the suggestions. I did umbrella simulation for 20ns and the pull force is as below. 19960.-6.78192 19962.33.3579 19964.-3.1808 19966.-15.0304 19968.-55.4436 19970.-38.9422 19972.-9.41927 19974.-5.95981 19976.0.626319 19978.2.28736 19980.23.5115 19982.10.6415 19984.-0.233446 19986.8.26525 19988.36.7656 19990.26.6017 19992.64.43 19994.53.3844 19996.18.3834 19998.39.8988 2.43.6291 I expect the force should be converged. my understanding might be wrong. I have poor knowledge about this umbrella sampling convergence and image selection for the PMF calculation. is this fluctuation in force due to pulling group motion out of box? can you give me some idea about the selection of images for PMF calculation? I found from the pullx files that the COM distance converges after few ns of simulation. I understood that we cant do PMF study with pull=constraint. Vijay. Message: 2 Date: Mon, 07 Nov 2011 09:07:21 -0500 From: chris.ne...@utoronto.ca Subject: [gmx-users] umbrella sampling with pull=constraint To: gmx-users@gromacs.org Message-ID: 2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list. Nevertheless, you do need to worry about which images are used to derive the pulling forces. You can often do that by a judicious selection of pull_pbcatom (read about that on-list and in the manual). In some cases, however, pull_pbcatom can not assist enough and you are forced to make the box larger. None of this is alleviated by pull=constraint, which is why I'm not going to answer your question about your .mdp parameters at this point. Let's get the problems identified and solved first with pull=umbrella. Chris. -- original message -- Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance between the reference and pulling group. Can we use pull=constraint option to retain the pulling group within the COM distance? my pulling code is as bellow with restrain at 0.5nm distance from ref group. I just want to get some idea about this pull code modification. pull= constraint pull_geometry= distance pull_dim= N N Y pull_start = no pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = Chain_B pull_init1 = 0.50 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 500 pull_nstfout= 500 Regards, Vijay. - -- 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: umbrella sampling with pull=constraint
and also I tried to plot the PMF curve from this data, I got few warning messages like no data point in bin 20, You may not get a reasonable profile. Check your histograms!. the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely overlaps at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm window to get the restrain distance converged? On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj vijayara...@gmail.com wrote: Hello, Thanks for the suggestions. I did umbrella simulation for 20ns and the pull force is as below. 19960.-6.78192 19962.33.3579 19964.-3.1808 19966.-15.0304 19968.-55.4436 19970.-38.9422 19972.-9.41927 19974.-5.95981 19976.0.626319 19978.2.28736 19980.23.5115 19982.10.6415 19984.-0.233446 19986.8.26525 19988.36.7656 19990.26.6017 19992.64.43 19994.53.3844 19996.18.3834 19998.39.8988 2.43.6291 I expect the force should be converged. my understanding might be wrong. I have poor knowledge about this umbrella sampling convergence and image selection for the PMF calculation. is this fluctuation in force due to pulling group motion out of box? can you give me some idea about the selection of images for PMF calculation? I found from the pullx files that the COM distance converges after few ns of simulation. I understood that we cant do PMF study with pull=constraint. Vijay. Message: 2 Date: Mon, 07 Nov 2011 09:07:21 -0500 From: chris.ne...@utoronto.ca Subject: [gmx-users] umbrella sampling with pull=constraint To: gmx-users@gromacs.org Message-ID: 2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list. Nevertheless, you do need to worry about which images are used to derive the pulling forces. You can often do that by a judicious selection of pull_pbcatom (read about that on-list and in the manual). In some cases, however, pull_pbcatom can not assist enough and you are forced to make the box larger. None of this is alleviated by pull=constraint, which is why I'm not going to answer your question about your .mdp parameters at this point. Let's get the problems identified and solved first with pull=umbrella. Chris. -- original message -- Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance between the reference and pulling group. Can we use pull=constraint option to retain the pulling group within the COM distance? my pulling code is as bellow with restrain at 0.5nm distance from ref group. I just want to get some idea about this pull code modification. pull= constraint pull_geometry= distance pull_dim= N N Y pull_start = no pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = Chain_B pull_init1 = 0.50 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 500 pull_nstfout= 500 Regards, Vijay. - -- 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: umbrella sampling with pull=constraint
Vijayaraj wrote: and also I tried to plot the PMF curve from this data, I got few warning messages like no data point in bin 20, You may not get a reasonable profile. Check your histograms!. the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely overlaps at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm window to get the restrain distance converged? It is still somewhat difficult to provide any useful advice. You haven't stated what your system is, how your windows were assembled, at what interval they exist, or how many you have. The above warnings suggest that you've either set up the windows wrong, have insufficient data, or are analyzing parts of the trajectory you shouldn't be (i.e. initial times that are equilibration). -Justin On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj vijayara...@gmail.com mailto:vijayara...@gmail.com wrote: Hello, Thanks for the suggestions. I did umbrella simulation for 20ns and the pull force is as below. 19960.-6.78192 19962.33.3579 19964.-3.1808 19966.-15.0304 19968.-55.4436 19970.-38.9422 19972.-9.41927 19974.-5.95981 19976.0.626319 19978.2.28736 19980.23.5115 19982.10.6415 19984.-0.233446 19986.8.26525 19988.36.7656 19990.26.6017 19992.64.43 19994.53.3844 19996.18.3834 19998.39.8988 2.43.6291 I expect the force should be converged. my understanding might be wrong. I have poor knowledge about this umbrella sampling convergence and image selection for the PMF calculation. is this fluctuation in force due to pulling group motion out of box? can you give me some idea about the selection of images for PMF calculation? I found from the pullx files that the COM distance converges after few ns of simulation. I understood that we cant do PMF study with pull=constraint. Vijay. Message: 2 Date: Mon, 07 Nov 2011 09:07:21 -0500 From: chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca Subject: [gmx-users] umbrella sampling with pull=constraint To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca mailto:2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list. Nevertheless, you do need to worry about which images are used to derive the pulling forces. You can often do that by a judicious selection of pull_pbcatom (read about that on-list and in the manual). In some cases, however, pull_pbcatom can not assist enough and you are forced to make the box larger. None of this is alleviated by pull=constraint, which is why I'm not going to answer your question about your .mdp parameters at this point. Let's get the problems identified and solved first with pull=umbrella. Chris. -- original message -- Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance between the reference and pulling group. Can we use pull=constraint option to retain the pulling group within the COM distance? my pulling code is as bellow with restrain at 0.5nm distance from ref group. I just want to get some idea about this pull code modification. pull= constraint pull_geometry= distance pull_dim= N N Y pull_start = no pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = Chain_B pull_init1 = 0.50 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 500 pull_nstfout= 500 Regards, Vijay. - -- 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] lipid bilayer and umbrella sampling
Dear Gromacs Users, I am trying to extract the potential of mean force of a small molecule in a DPPC bilayer. To this end, I applied the methodology described in an online manual written by Justin Lemkul. My problem is when I run biasing simulations of the molecule near the interface (DPPC/water), some lipid molecules move to the water phase. This has as a consequence a local disorder of the bilayer. Below is the parameters I employ for the pull code: pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = DPPC pull_group1 = DTC pull_rate1 = 0.0 pull_k1 = 1000 Is the position restraints on DPPC molecules a solution to my problem? Thanks in advance Best regards Giovani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein - ligand
On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Center on either the protein, the ligand, or some custom index group of residues surrounding the ligand. Centering on the whole system usually doesn't do anything useful. -Justin Thank you guys but... I am trying and it does not work... my ligand is jumping like an idiot outside the box changing its position even two dimensions of box in one frame. I removed -ur compact from the first line and I tried centering on ligand or protein (centering group: LIG or Protein, output: SYSTEM). No results... My ligand at the begining of the simualtion is not within the protein. Please, help : I tried this workflow with many ligands and same protein - it worked! Now it does not... Here is my workflow: 1. First make your molecules whole if you want them whole. trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step (tried centering on LIG or PROTEIN) trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc With point three, the issue is that trjconvhttp://www.gromacs.org/Documentation/Gromacs_Utilities/trjconvremoves the jumps from the first frame using the reference structure provided with -s. If the reference structure (run input file) is not clustered/whole, trjconv -pbc nojump will undo steps 1 and Steven ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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: umbrella sampling with pull=constraint
My system is a self-assembled cyclic peptide, I am trying to extract PMF to pull one of the terminal cyclic peptide. I have collected 25 windows starting from 0.5nm with 0.05nm window size. the histogram shows up to 0.7nm all the windows are overlapped around 0.5nm, and poor sampling from 0.6 to 0.75nm. from 0.75nm the sampling is perfect. each cyclic peptide has 8 residues and the terminal one forms 8 hbonds with the 2nd cyclic peptide. I guess due to this strong hbonding, the sampling window up to 0.7nm is very poor. If we extend the simulation only for these windows can we get proper sampling windows? this observation is from last 10ns of 20ns simulation. Message: 3 Date: Mon, 07 Nov 2011 10:20:07 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: umbrella sampling with pull=constraint To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4eb7f727.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Vijayaraj wrote: and also I tried to plot the PMF curve from this data, I got few warning messages like no data point in bin 20, You may not get a reasonable profile. Check your histograms!. the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely overlaps at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm window to get the restrain distance converged? It is still somewhat difficult to provide any useful advice. You haven't stated what your system is, how your windows were assembled, at what interval they exist, or how many you have. The above warnings suggest that you've either set up the windows wrong, have insufficient data, or are analyzing parts of the trajectory you shouldn't be (i.e. initial times that are equilibration). -Justin On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj vijayara...@gmail.com mailto:vijayara...@gmail.com wrote: Hello, Thanks for the suggestions. I did umbrella simulation for 20ns and the pull force is as below. 19960.-6.78192 19962.33.3579 19964.-3.1808 19966.-15.0304 19968.-55.4436 19970.-38.9422 19972.-9.41927 19974.-5.95981 19976.0.626319 19978.2.28736 19980.23.5115 19982.10.6415 19984.-0.233446 19986.8.26525 19988.36.7656 19990.26.6017 19992.64.43 19994.53.3844 19996.18.3834 19998.39.8988 2.43.6291 I expect the force should be converged. my understanding might be wrong. I have poor knowledge about this umbrella sampling convergence and image selection for the PMF calculation. is this fluctuation in force due to pulling group motion out of box? can you give me some idea about the selection of images for PMF calculation? I found from the pullx files that the COM distance converges after few ns of simulation. I understood that we cant do PMF study with pull=constraint. Vijay. Message: 2 Date: Mon, 07 Nov 2011 09:07:21 -0500 From: chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca Subject: [gmx-users] umbrella sampling with pull=constraint To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca mailto:2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list. Nevertheless, you do need to worry about which images are used to derive the pulling forces. You can often do that by a judicious selection of pull_pbcatom (read about that on-list and in the manual). In some cases, however, pull_pbcatom can not assist enough and you are forced to make the box larger. None of this is alleviated by pull=constraint, which is why I'm not going to answer your question about your .mdp parameters at this point. Let's get the problems identified and solved first with pull=umbrella. Chris. -- original message -- Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not
[gmx-users] request for comments on profile.xvg (PMF) courve
Dear gmx users, my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of which one is pulled from the other. I followed Justin's tutorial on umbrella sampling. Here are the results. profile.xvg: http://przemekbartha.pl/upload/profile.png histo.xvg: http://przemekbartha.pl/upload/histo.png I would be grateful, if anyone could tell me why is the PMF so irregular, unstable, unlike the courve in the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/07_analysis.html After a little bit of research on gmx-users, my guess is either incorrent sampling or/and some major mistake in parametrization. I tried to resample the simulation so that the umbrellas don't overlap as much as they do in my histo.xvg file but it changed the PMF totaly and did not resolve the problem. Or maybe, it is just the way it should be? My pullcode is nearly the same as in the tutorial. I don't want to trash, but if you require any additional information, please let me know. The sampling is twice as small as in the tutorial since my computational resources are limited, but when I tried running more precise sampling, the results were pretty much the same (irregular courve). Thanks in advance. Przemek part of md_umbrella.mdp: ; Run parameters integrator = md dt = 0.004 tinit = 0 nsteps = 250 ; 10 ns ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps-- 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] lipid bilayer and umbrella sampling
Giovanni Mancini wrote: Dear Gromacs Users, I am trying to extract the potential of mean force of a small molecule in a DPPC bilayer. To this end, I applied the methodology described in an online manual written by Justin Lemkul. My problem is when I run biasing simulations of the molecule near the interface (DPPC/water), some lipid molecules move to the water phase. This has as a consequence a local disorder of the bilayer. Below is the parameters I employ for the pull code: pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = DPPC pull_group1 = DTC pull_rate1 = 0.0 pull_k1 = 1000 Is the position restraints on DPPC molecules a solution to my problem? It's certainly the most immediate solution that comes to my mind. Try it and see if it alleviates your issue. -Justin -- 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: umbrella sampling with pull=constraint
Vijayaraj wrote: My system is a self-assembled cyclic peptide, I am trying to extract PMF to pull one of the terminal cyclic peptide. I have collected 25 windows starting from 0.5nm with 0.05nm window size. the histogram shows up to 0.7nm all the windows are overlapped around 0.5nm, and poor sampling from 0.6 to 0.75nm. from 0.75nm the sampling is perfect. each cyclic peptide has 8 residues and the terminal one forms 8 hbonds with the 2nd cyclic peptide. I guess due to this strong hbonding, the sampling window up to 0.7nm is very poor. If we extend the simulation only for these windows can we get proper sampling windows? this observation is from last 10ns of 20ns simulation. It sounds like you need a substantially stronger force constant to restrain the positions where the sampling is failing. -Justin Message: 3 Date: Mon, 07 Nov 2011 10:20:07 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Re: umbrella sampling with pull=constraint To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4eb7f727.3000...@vt.edu mailto:4eb7f727.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Vijayaraj wrote: and also I tried to plot the PMF curve from this data, I got few warning messages like no data point in bin 20, You may not get a reasonable profile. Check your histograms!. the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely overlaps at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm window to get the restrain distance converged? It is still somewhat difficult to provide any useful advice. You haven't stated what your system is, how your windows were assembled, at what interval they exist, or how many you have. The above warnings suggest that you've either set up the windows wrong, have insufficient data, or are analyzing parts of the trajectory you shouldn't be (i.e. initial times that are equilibration). -Justin On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj vijayara...@gmail.com mailto:vijayara...@gmail.com mailto:vijayara...@gmail.com mailto:vijayara...@gmail.com wrote: Hello, Thanks for the suggestions. I did umbrella simulation for 20ns and the pull force is as below. 19960.-6.78192 19962.33.3579 19964.-3.1808 19966.-15.0304 19968.-55.4436 19970.-38.9422 19972.-9.41927 19974.-5.95981 19976.0.626319 19978.2.28736 19980.23.5115 19982.10.6415 19984.-0.233446 19986.8.26525 19988.36.7656 19990.26.6017 19992.64.43 19994.53.3844 19996.18.3834 19998.39.8988 2.43.6291 I expect the force should be converged. my understanding might be wrong. I have poor knowledge about this umbrella sampling convergence and image selection for the PMF calculation. is this fluctuation in force due to pulling group motion out of box? can you give me some idea about the selection of images for PMF calculation? I found from the pullx files that the COM distance converges after few ns of simulation. I understood that we cant do PMF study with pull=constraint. Vijay. Message: 2 Date: Mon, 07 Nov 2011 09:07:21 -0500 From: chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca Subject: [gmx-users] umbrella sampling with pull=constraint To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca mailto:2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca mailto:2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca mailto:2007090721.jy8zfzhvh4ccw...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed
Re: [gmx-users] request for comments on profile.xvg (PMF) courve
Przemek Bartha wrote: Dear gmx users, my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of which one is pulled from the other. I followed Justin's tutorial on umbrella sampling. Here are the results. profile.xvg: http://przemekbartha.pl/upload/profile.png histo.xvg: http://przemekbartha.pl/upload/histo.png I would be grateful, if anyone could tell me why is the PMF so irregular, unstable, unlike the courve in the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/07_analysis.html After a little bit of research on gmx-users, my guess is either incorrent sampling or/and some major mistake in parametrization. I tried to resample the simulation so that the umbrellas don't overlap as much as they do in my histo.xvg file but it changed the PMF totaly and did not resolve the problem. Or maybe, it is just the way it should be? Overlap between the histograms is what you want. If your histograms do not overlap, then you get poor results. My pullcode is nearly the same as in the tutorial. I don't want to trash, but if you require any additional information, please let me know. The sampling is twice as small as in the tutorial since my computational resources are limited, but when I tried running more precise sampling, the results were pretty much the same (irregular courve). Based on the histogram counts, it seems like you have an order of magnitude less sampling than the tutorial. I suspect it is because you've doubled the value of dt (below) without accounting for this fact. You may need to either (1) simulate for longer or (2) save snapshots more often. I suspect the former is more likely to be useful. -Justin Thanks in advance. Przemek part of md_umbrella.mdp: ; Run parameters integrator = md dt = 0.004 tinit = 0 nsteps = 250 ; 10 ns ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps -- 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] problem while running production md
dear gmx-users, i am getting the following error message while running production md (mpirun).. Step 102, time 0.204 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5079 5069 30.70.1532 0.1888 0.1522 5081 5079 79.80.1056 0.2608 0.1335 5080 5079 39.10.1237 0.1673 0.1229 5083 5081 79.70.1459 0.8597 0.1449 5082 5081 78.70.1016 0.1856 0.1010 5098 5083 78.50.1532 0.7685 0.1522 5085 5083 85.90.1537 1.9840 0.1526 5084 5083 70.40.1097 0.4235 0.1090 5088 5085 83.60.1536 2.4114 0.1526 5087 5085 85.90.1098 1.5565 0.1090 5086 5085 87.30.1099 1.2617 0.1090 5088 5094 88.60.1535 3.0328 0.1526 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 5093 and 5094 at distance 6.570 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 5091 and 5094 at distance 2.444 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Fatal error: 1 particles communicated to PME node 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. any suggestion to get rid of this problem Ansuman Biswas Physics Department Indian Institute of Science Bangalore India -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] problem while running production md
ansu...@physics.iisc.ernet.in wrote: dear gmx-users, i am getting the following error message while running production md (mpirun).. Step 102, time 0.204 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5079 5069 30.70.1532 0.1888 0.1522 5081 5079 79.80.1056 0.2608 0.1335 5080 5079 39.10.1237 0.1673 0.1229 5083 5081 79.70.1459 0.8597 0.1449 5082 5081 78.70.1016 0.1856 0.1010 5098 5083 78.50.1532 0.7685 0.1522 5085 5083 85.90.1537 1.9840 0.1526 5084 5083 70.40.1097 0.4235 0.1090 5088 5085 83.60.1536 2.4114 0.1526 5087 5085 85.90.1098 1.5565 0.1090 5086 5085 87.30.1099 1.2617 0.1090 5088 5094 88.60.1535 3.0328 0.1526 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 5093 and 5094 at distance 6.570 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 5091 and 5094 at distance 2.444 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Fatal error: 1 particles communicated to PME node 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. any suggestion to get rid of this problem Please search the Gromacs website, where this issue is discussed in some depth, and/or search the list archive to find any of the thousands of posts where this issue has been solved before. -Justin -- 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] lipid bilayer and umbrella sampling
If you add position restraints to your DPPC molecules, then you are changing your effective order parameter. The PMF for the solute along the normal to a restrained bilayer will have a different shape than a PMF for the solute along the normal to an urestrained bilayer. Whether or not this is a problem will depend on the question that you are trying to answer. If the bilayer is falling apart, then you certainly need to do something. But if it is just locally ordering/disordering, then I don't see the big problem, besides the effect that this has on convergence (DOI: 10.1021/ct200316w). Chris. -- original message -- Dear Gromacs Users, I am trying to extract the potential of mean force of a small molecule in a DPPC bilayer. To this end, I applied the methodology described in an online manual written by Justin Lemkul. My problem is when I run biasing simulations of the molecule near the interface (DPPC/water), some lipid molecules move to the water phase. This has as a consequence a local disorder of the bilayer. Below is the parameters I employ for the pull code: pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = DPPC pull_group1 = DTC pull_rate1 = 0.0 pull_k1 = 1000 Is the position restraints on DPPC molecules a solution to my problem? Thanks in advance Best regards Giovani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein - ligand
Hi Steven, Step 2: Cluster your molecules. This is where you have to forge a reference frame that you can use to remove jumps from your trajectory. If the ligand is not with the protein at the start, you'll have to shift it so that it is. Maybe -pbc cluster is your friend there. I do assume that the ligand is really with the protein and not in the solvent... Cheers, Tsjerk On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Center on either the protein, the ligand, or some custom index group of residues surrounding the ligand. Centering on the whole system usually doesn't do anything useful. -Justin Thank you guys but... I am trying and it does not work... my ligand is jumping like an idiot outside the box changing its position even two dimensions of box in one frame. I removed -ur compact from the first line and I tried centering on ligand or protein (centering group: LIG or Protein, output: SYSTEM). No results... My ligand at the begining of the simualtion is not within the protein. Please, help : I tried this workflow with many ligands and same protein - it worked! Now it does not... Here is my workflow: 1. First make your molecules whole if you want them whole. trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step (tried centering on LIG or PROTEIN) trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc With point three, the issue is that trjconv removes the jumps from the first frame using the reference structure provided with -s. If the reference structure (run input file) is not clustered/whole, trjconv -pbc nojump will undo steps 1 and Steven 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 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-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
[gmx-users] Re: PBC - Protein - ligand
Hi Tsjerk, Thank you. Unfortunately my ligand is not with protein. I put my ligand around my protein (in water) running separate simulations to see where can it bind. It is close to protein but not within. Any other suggestion? I used also pbc -res so I observe my ligand close to protein but sometimes still changing its position rapidly... No clue for now how to solve it... Steven On Monday, November 7, 2011, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Steven, Step 2: Cluster your molecules. This is where you have to forge a reference frame that you can use to remove jumps from your trajectory. If the ligand is not with the protein at the start, you'll have to shift it so that it is. Maybe -pbc cluster is your friend there. I do assume that the ligand is really with the protein and not in the solvent... Cheers, Tsjerk On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Center on either the protein, the ligand, or some custom index group of residues surrounding the ligand. Centering on the whole system usually doesn't do anything useful. -Justin Thank you guys but... I am trying and it does not work... my ligand is jumping like an idiot outside the box changing its position even two dimensions of box in one frame. I removed -ur compact from the first line and I tried centering on ligand or protein (centering group: LIG or Protein, output: SYSTEM). No results... My ligand at the begining of the simualtion is not within the protein. Please, help : I tried this workflow with many ligands and same protein - it worked! Now it does not... Here is my workflow: 1. First make your molecules whole if you want them whole. trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step (tried centering on LIG or PROTEIN) trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
[gmx-users] gromacs query for force field in vaccum and liquid
I want to simulate membrane protein in vaccum so let me know which force field i can use for it. Also I m doing simulation for the same protein in liquid using OPLS force field.Please tell me is it correct? -- 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 while running production md
dear gmx-users, i am getting the following error message while running production md (mpirun).. Step 102, time 0.204 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5079 5069 30.7 0.1532 0.1888 0.1522 5081 5079 79.8 0.1056 0.2608 0.1335 5080 5079 39.1 0.1237 0.1673 0.1229 5083 5081 79.7 0.1459 0.8597 0.1449 5082 5081 78.7 0.1016 0.1856 0.1010 5098 5083 78.5 0.1532 0.7685 0.1522 5085 5083 85.9 0.1537 1.9840 0.1526 5084 5083 70.4 0.1097 0.4235 0.1090 5088 5085 83.6 0.1536 2.4114 0.1526 5087 5085 85.9 0.1098 1.5565 0.1090 5086 5085 87.3 0.1099 1.2617 0.1090 5088 5094 88.6 0.1535 3.0328 0.1526 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 5093 and 5094 at distance 6.570 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 5091 and 5094 at distance 2.444 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I think your system is not relaxed, so you are NOT actually running production md. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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: PBC - Protein - ligand
Steven Neumann wrote: Hi Tsjerk, Thank you. Unfortunately my ligand is not with protein. I put my ligand around my protein (in water) running separate simulations to see where can it bind. It is close to protein but not within. Any other suggestion? I used also pbc -res so I observe my ligand close to protein but sometimes still changing its position rapidly... No clue for now how to solve it... I have no idea why the proposed protocol isn't working, but I know that one should be able to do something very simple, along the lines of the following, for this to work: 1. trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol 2. trjconv -s md.tpr -f pbc_fix.xtc -o center.xtc -center (center on the protein) 3. trjconv -s md.tpr -f center.xtc -o fit.xtc -fit rot+trans (choose protein for fitting) -Justin Steven On Monday, November 7, 2011, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Steven, Step 2: Cluster your molecules. This is where you have to forge a reference frame that you can use to remove jumps from your trajectory. If the ligand is not with the protein at the start, you'll have to shift it so that it is. Maybe -pbc cluster is your friend there. I do assume that the ligand is really with the protein and not in the solvent... Cheers, Tsjerk On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Center on either the protein, the ligand, or some custom index group of residues surrounding the ligand. Centering on the whole system usually doesn't do anything useful. -Justin Thank you guys but... I am trying and it does not work... my ligand is jumping like an idiot outside the box changing its position even two dimensions of box in one frame. I removed -ur compact from the first line and I tried centering on ligand or protein (centering group: LIG or Protein, output: SYSTEM). No results... My ligand at the begining of the simualtion is not within the protein. Please, help : I tried this workflow with many ligands and same protein - it worked! Now it does not... Here is my workflow: 1. First make your molecules whole if you want them whole. trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step (tried centering on LIG or PROTEIN) trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced
[gmx-users] Water Liquid-vapor interface: Negative surface tension by virial formula?
Dear GMXers, I'm computing the liquid-vapor surface tension for SPC/E water using GROMACS 4.5.3. The initial water box dimension is 3nm*3nm*3nm, containing 1807 water molecules, which is extended in z direction to a length of 12nm, to create two liquid-vapor interfaces. The ensemble is NVT. The system was equilibrated for 1ns and ran for 60ns for data collection. Below is the pressure and virial output using g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Vir-XX 4809.71.3721.805 -5.05917 (kJ/mol) Vir-YY 4810.68 1723.077 -3.29302 (kJ/mol) Vir-ZZ 4536.490.1715.838 -0.434853 (kJ/mol) Pres-XX-97.9413 0.39223.717 1.4721 (bar) Pres-YY-98.2664 0.33224.0851.21738 (bar) Pres-ZZ -0.204398 0.012221.921 0.0134426 (bar) If I compute the surface tension using gamma = (pzz-0.5*(pxx+pyy))*Lz/2, the resulting surface tension is 58.7mN/m. But if the surface tension is computed using gamma=(PIzz-0.5*(PIxx+PIyy))/Axy, the resulting surface tension is -25.3mN/m, which is negative. Is there anything wrong with my calculation? I will be happy to provide any further information regarding the simulation setup if needed. Thank you in advance. Best, Yanbin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein - ligand
On 8/11/2011 3:17 AM, Steven Neumann wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Center on either the protein, the ligand, or some custom index group of residues surrounding the ligand. Centering on the whole system usually doesn't do anything useful. -Justin Thank you guys but... I am trying and it does not work... my ligand is jumping like an idiot outside the box changing its position even two dimensions of box in one frame. I have no idea what you mean by this. I removed -ur compact from the first line and I tried centering on ligand or protein (centering group: LIG or Protein, output: SYSTEM). No results... My ligand at the begining of the simualtion is not within the protein. Please, help : I tried this workflow with many ligands and same protein - it worked! Now it does not... Sure. So far you've given us no understanding of what your ligand is doing during the simulation. If you don't know either, go and look at it. Then go and look at the trajectory from each stage of your work flow and see what it looks like and how things are changing. Then when something looks wrong you have a single step you can trouble shoot... maybe the operation is not sensible, maybe the way you did it is wrong, maybe the code is wrong. You cannot expect to transfer work flows from another simulation without considering what is happening in this one. Scenarios where your ligand is diffusing away from your protein and reassociating to another side require different work flows from one where the ligand stays nearby a binding pocket. In the latter, you should probably use -pbc cluster in step 2, though some of the time it won't matter. In the former, using -nojump to allow diffusion out of the box, and then step 6 to put everything back in the box doesn't make sense. Just doing operations and selecting groups without considering the nature of the operation will get a garbage result. There's a good reason mdrun doesn't attempt to second-guess how you would like all of this done! Mark Here is my workflow: 1.First make your molecules whole if you want them whole. trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc 2.Cluster your molecules/particles if you want them clustered 3.Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4.Remove jumps if you want to have them removed using the first frame (system) trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5.Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc|nojump|after this step (tried centering on LIG or PROTEIN) trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc 6.Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7.Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc With point three, the issue is that trjconv http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv removes the jumps from the first frame using the reference structure provided with |-s|. If the reference structure (run input file) is not
Re: [gmx-users] gromacs query for force field in vaccum and liquid
On 8/11/2011 8:24 AM, Anushree Tripathi wrote: I want to simulate membrane protein in vaccum so let me know which force field i can use for it. Probably none of them - they were all parametrized on condensed-phase data. In order to do such a simulation, you are going to have to establish a valid protocol for so doing, and that means finding similar work in the literature. So you will need to go and find such work. That will begin to address the issue of force field choice. Also I m doing simulation for the same protein in liquid using OPLS force field.Please tell me is it correct? OPLS has some demonstrated value for condensed-phase simulations. Whether it is a valid or best choice for your context depends on a great many things that you haven't mentioned yet, and that we wouldn't have time to address if you had :-) Reading about what other people with more experience than you have done is a necessary learning process. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond -hbn
Hi Gmxers, I used g_hbond -n protein.ndx -hbn output.xvg to get the index of all the atoms forming H-bond with the protein, but since H-Bonds should be dynamic as time evolves, I should see changing number of HBonds in the output.xvg which I have not seen yet. Kinda confused. Thanks, Yao -- 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] g_hbond -hbn
Yao Yao wrote: Hi Gmxers, I used g_hbond -n protein.ndx -hbn output.xvg to get the index of all the atoms forming H-bond with the protein, but since H-Bonds should be dynamic as time evolves, I should see changing number of HBonds in the output.xvg which I have not seen yet. Kinda confused. The output of -hbn is an index file, not an .xvg file. The index file can be mapped to the output of -hbm, which is an existence matrix of the hydrogen bonds. Some may swap simultaneously, so you may not see dramatic changes in the output of -num (the number of hydrogen bonds). -Justin -- 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] B-factor to large? Input for TLS
On 5/11/2011 11:05 AM, Henri Mone wrote: Dear Gromacs Users and Experts, I want to calculate from my xtc trajectory the B-factor and the anisotropic temperature factor. I'm using following gromacs command: $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb Does this reference structure in -s make sense for the trajectory supplied for -f? If the computed atomic deviations make no sense, then neither will the fluctuations. I have no idea if g_rmsf takes proper account of periodicity, but you might need either to massage the trajectory suitably with trjconv (see website for suggested workflows), or supply a .tpr with the correct box information. I want to input the resulting PDB file to the TLS Server [1] to calculate the hinge residues for my system. The B-factor which g_rmsf is calculating seem to be to large, they are in the range of 2000 to 6000 (last column without the 1.00 prefix) [2]. The website [3] suggests that a reasonable B-factor should is in the range of 21 to 200. Also the TLS server [1] complains that the b-factors are in the wrong range. I did several test but I have no idea what Im doing wrong. The trajectory is with 250ns long enough to get for my small system a convergence on the B-factor. - I thought it could be a unit problem, what are the B-factor units which g_rmsf uses? Could this cause such an huge difference in the b-factor? g_rmsf converts to Angstroms before writing B-factor output to PDB, as you would expect. Mark - What is the standard unit for the b-factor in the PDB definition (from the PDB database)? - What is a realistic range for the b-factor? - What else could be the error source, what am I doing wrong? Thanks, any help is welcome, Henrey ---1: TLSMD SERVER http://skuld.bmsc.washington.edu/~tlsmd/ ---2: bfac2.pdb : ... ATOM 6146 N GLY 435 97.841 52.072 37.712 1.006712.85 ATOM 6147 HN GLY 435 97.972 52.020 37.437 1.006676.79 ATOM 6148 CA GLY 435 97.953 52.003 37.883 1.006739.30 ATOM 6149 HA1 GLY 435 97.975 51.822 37.563 1.006956.61 ATOM 6150 HA2 GLY 435 97.554 52.041 37.972 1.007042.78 ATOM 6151 C GLY 435 98.601 52.111 38.350 1.006210.20 ATOM 6152 O GLY 435 98.552 51.909 38.905 1.006278.92 ATOM 6153 N ASN 436 99.235 52.437 38.127 1.005772.75 ATOM 6154 HN ASN 436 99.262 52.602 37.668 1.005803.67 ATOM 6155 CA ASN 436 99.904 52.574 38.508 1.005343.12 ATOM 6156 HA ASN 436 99.947 52.400 38.918 1.005671.18 ATOM 6157 CB ASN 436 100.537 52.527 37.948 1.005355.63 ATOM 6158 HB1 ASN 436 100.960 52.556 38.127 1.005098.00 ATOM 6159 HB2 ASN 436 100.553 52.657 37.601 1.005272.78 ATOM 6160 CG ASN 436 100.587 52.258 37.586 1.006031.62 ATOM 6161 OD1 ASN 436 100.582 52.138 37.675 1.006435.18 ATOM 6162 ND2 ASN 436 100.641 52.163 37.176 1.006306.09 ATOM 6163 1HD2 ASN 436 100.689 51.993 36.928 1.006834.63 ATOM 6164 2HD2 ASN 436 100.652 52.264 37.117 1.006062.64 ATOM 6165 C ASN 436 99.947 53.023 38.917 1.004590.56 ATOM 6166 O ASN 436 99.651 53.240 38.597 1.004290.70 ... ---3: B-factor range at 3 Å resolution http://www.p212121.com/2009/04/12/b-factor-range-3-resolution/ -- 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] Problems with deuterium graphs
Dear All, I run a MD simulation on a membrane protein using DPPC and I performed a deuterium order parameters on the trajectory. As I'm a newbie, could you kindly help me to give an interpretation of these graphs? You can open them at: sn1 http://www.freeimagehosting.net/137c9 sn2 http://www.freeimagehosting.net/6e321 Thanks in advance -- 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] Sorry for posting twice
I'm sorry for having post the message about deuterium twice. It ws a mistake -- 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 question about deuteriu order parameters graph
Dear All, I run a MD simulation on a membrane protein using DPPC and I performed a deuterium order parameters on the trajectory. As I'm a newbie, could you kindly help me to give an interpretation of these graphs? You can open them at: sn1 http://www.freeimagehosting.net/137c9 sn2 http://www.freeimagehosting.net/6e321 Thanks in advance -- 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] how to make topol.top file for mixed solution
Dear, I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by using two comands: *genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p mibc.top* then I filled this mixture by water to create other 5 5 10 box by using comands: *genbox -cp mix.gro -cs spc216.gro -o box1.g96 -p topol.top -box 5 5 10* the topol.top file is: *#include ffG43a1.itp #include decanol.itp #include mibc.itp ; include water #include spce.itp [ system ] MIBC and dec in water [ molecules ] dec 15 mibc 15 sol 7947.* then I ran the grompp comand: grompp -f input_min.mdp -o min.tpr -c box1.g96 and the errors was *Warning: atom name 2 in topol.top and box1.g96 does not match (CAC - CAF)* *Warning: atom name 3 in topol.top and box1.g96 does not match (CAE - CAB)* *Warning: atom name 4 in topol.top and box1.g96 does not match (CAG - CAE)* *Warning: atom name 5 in topol.top and box1.g96 does not match (CAI - CAG)* *Warning: atom name 6 in topol.top and box1.g96 does not match (CAK - CAC)* *Warning: atom name 7 in topol.top and box1.g96 does not match (CAJ - OAD)* *Warning: atom name 8 in topol.top and box1.g96 does not match (CAH - HAN)* *Warning: atom name 9 in topol.top and box1.g96 does not match (CAF - CAA)* *Warning: atom name 10 in topol.top and box1.g96 does not match (CAD - CAF)* *WARNING 1 [file topol.top, line 20]:* * 220 non-matching atom names* * atom names from topol.top will be used* * atom names from box1.g96 will be ignored* *--- * *Fatal error:* *Too many warnings (2), grompp terminated.* *If you are sure all warnings are harmless, use the -maxwarn option.* *For more information and tips for troubleshooting, please check the GROMACS * *website at http://www.gromacs.org/Documentation/Errors * Please help me to correct these errors. Thank you very much best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu cuong nguyen wrote: Dear, Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system. So please help me to create a suitable topol.top file to this system. No one can help you without knowing the exact errors that grompp produced. -Justin Thanks a lot. Best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Justin A. Lemkul wrote: cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please read the tutorial: http://www.gromacs.org/__**Documentation/Tutorials#__** Heterogeneous_Systemshttp://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems http://www.gromacs.org/**Documentation/Tutorials#** Heterogeneous_Systemshttp://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems Also possibly useful: http://www.gromacs.org/__**Documentation/How-tos/Mixed___**Solventshttp://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents http://www.gromacs.org/**Documentation/How-tos/Mixed_**Solventshttp://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read
[gmx-users] remd with different potential at different temperature
dear teacher, how can i do remd with different non-bond potential at different temperature ? easy to say ,can i use different *.top at diferent temperature. if not ,can you give me some suggestions to rewrite the gromacs codes. thanks!! regards, PHD, Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com -- 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] how to make topol.top file for mixed solution
On 8/11/2011 5:36 PM, cuong nguyen wrote: Dear, I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by using two comands: /genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p mibc.top/ The -ci value for this command would insert more decanol, not mibc. then I filled this mixture by water to create other 5 5 10 box by using comands: /genbox -cp mix.gro -cs spc216.gro -o box1.g96 -p topol.top -box 5 5 10/ Where did mix.gro come from? If you want to encourage people to help you, these commands should be copied and pasted from your terminal (or the shell script you wrote so that your procedure was self-documenting). Otherwise we've got no reason to suppose your reported input and your reported output have any causal relationship between them. The more things you filter through your head each time, the more errors you will make - and that goes for more than workflows for getting help! :) the topol.top file is: /#include ffG43a1.itp #include decanol.itp #include mibc.itp ; include water #include spce.itp [ system ] MIBC and dec in water [ molecules ] dec 15 mibc 15 sol 7947./ then I ran the grompp comand: grompp -f input_min.mdp -o min.tpr -c box1.g96 and the errors was /Warning: atom name 2 in topol.top and box1.g96 does not match (CAC - CAF)/ /Warning: atom name 3 in topol.top and box1.g96 does not match (CAE - CAB)/ /Warning: atom name 4 in topol.top and box1.g96 does not match (CAG - CAE)/ /Warning: atom name 5 in topol.top and box1.g96 does not match (CAI - CAG)/ /Warning: atom name 6 in topol.top and box1.g96 does not match (CAK - CAC)/ /Warning: atom name 7 in topol.top and box1.g96 does not match (CAJ - OAD)/ /Warning: atom name 8 in topol.top and box1.g96 does not match (CAH - HAN)/ /Warning: atom name 9 in topol.top and box1.g96 does not match (CAF - CAA)/ /Warning: atom name 10 in topol.top and box1.g96 does not match (CAD - CAF)/ /WARNING 1 [file topol.top, line 20]:/ /220 non-matching atom names/ /atom names from topol.top will be used/ /atom names from box1.g96 will be ignored/ /--- / /Fatal error:/ /Too many warnings (2), grompp terminated./ /If you are sure all warnings are harmless, use the -maxwarn option./ /For more information and tips for troubleshooting, please check the GROMACS/ /website at http://www.gromacs.org/Documentation/Errors / Please help me to correct these errors. The order of the [molecules] section of the grompp -p file must match the order in the grompp -c file. The order of the atoms within the [moleculetype] sections must likewise match the order in the grompp -c file. Yours don't, for some reason. You will have to look at these orderings and deduce what is wrong. Mark Thank you very much best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu cuong nguyen wrote: Dear, Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system. So please help me to create a suitable topol.top file to this system. No one can help you without knowing the exact errors that grompp produced. -Justin Thanks a lot. Best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu Justin A. Lemkul wrote: cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please read the tutorial: http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems Also possibly useful: http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080
Re: [gmx-users] remd with different potential at different temperature
On 8/11/2011 5:43 PM, ?? wrote: dear teacher, how can i do remd with different non-bond potential at different temperature ? easy to say ,can i use different *.top at diferent temperature. Probably. Try a simple case and see. The REMD implementation checks only certain critical quantities are constant over the generalized ensemble. See the lines that begin Multi-checking in an REMD .log file. You can probably even use different tabulated potentials for each replica. Mark if not ,can you give me some suggestions to rewrite the gromacs codes. thanks!! regards, PHD, Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com mailto:2008d...@gmail.com -- 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: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
= 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse = no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2007/8c5c63c5/attachment-0004.html -- -- 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! End of gmx-users Digest, Vol 91, Issue 36 * -- 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 -下面为附件内容- -- 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
