Re: [gmx-users] Pulling a CG protein
Hi Johnny, I am not familiar with pulling and even less with gromacs but I would be very cautious in using the MARTINI force field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested in knowing how it actually perform. XAvier. On Jul 30, 2009, at 1:04 AM, Johnny Lam wrote: Dear gromacs users, Hi, I am trying to pull apart a relatively large protein (CG using the martini force field) by pulling on two groups in opposite directions. To do this, I will be using the following .mdp file. However, I am almost certain that it contains errors: title= Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 17000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 2500 nstvout = 2500 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; MARTINI - no need for more frequent updates ; or larger neighborlist cut-off due ; to the use of shifted potential energy functions. ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; MARTINI - vdw and electrostatic interactions are used ; in their shifted forms. Changing to other types of ; electrostatics will affect the general performance of ; the model. ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; MARTINI - normal temperature and pressure coupling schemes ; can be used. It is recommended to couple individual groups ; in your system seperately. ; Temperature coupling = tcoupl = V-Rescale ; Groups to couple separately = tc-grps = PROTEIN W ; Time constant (ps) and reference temperature (K) = tau_t= 0.3 0.3 ref_t= 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 3.0 compressibility = 3e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 323 gen_seed = 666 ; OPTIONS FOR BONDS = ; MARTINI - for ring systems constraints are defined ; which are best handled using Lincs. constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 60 ; FREEZE GROUP ; Pulling pull= afm pull_geometry = direction pull_start = no pull_nstxout= 10 pull_nstfout= 10 pull_ngroups= 2 pull_group0 = pull_group1 = pull pull_vec1 = -0.1764 -0.9823 -0.0625 pull_init1 = -0.1764 -0.9823 -0.0625 pull_rate1 = 0.0001 pull_k1 = 1000 pull_group2 = freeze pull_vec2 = 0.1764 0.9823 0.0625 pull_init2 = 0.1764 0.9823 0.0625 pull_rate2 = 0.01 pull_k2 = 5000 The reason why group 2
Re: [gmx-users] Pulling a CG protein
Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these models have never been parameterized or systematically tested with this kind of application in mind. What I mean by qualitatively is that I wouldn't trust a force-extension curve of such simulations (unless you do some force-matching :)) - re: FD144), but the conformational changes that are observed in a moderate pulling regime do seem to make sense. The experiments we carried out were interactive pulling experiments, either to induce opening and closure of the guanylate kinase enzyme or to explore the membrane anchoring and the mechanical properties of the SNARE complex. This is briefly described in reference [1]. Cheers, Marc [1] http://dx.doi.org/10.1002/jcc.21235 O. Delalande, N. Férey, G. Grasseau and M. Baaden: Complex Molecular Assemblies at hand via Interactive Simulations, 2009, J. Comp. Chem. x.peri...@rug.nl said: Hi Johnny, I am not familiar with pulling and even less with gromacs but I would be very cautious in using the MARTINI force field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested in knowing how it actually perform. XAvier. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pulling a CG protein
Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these models have never been parameterized or systematically tested with this kind of application in mind. In general models that have been parameterized for one specific observable may not reproduce other observables *unless* the observables used for parameterization have a clear physical basis *and* the energy function captures the correct physics. Most biomolecular force fields (including Martini as far as I know) have been parameterized to reproduce density and energy of condensed phase (liquids), and hence this kind of data is usually reproduced quite well. However mixtures of components (e.g. two liquids) are usually not reproduced as well. By doing the kind of pulling simulations, preferably both atomistic and with CG models, one can try to verify whether the CG models can actually reproduce force curves to a comparable accuracy as all atom models. This kind of work should be done *systematically* before any applications. What does this boil down to? If you want to apply MD tools to get an accurate force curve *now*, use all atom models. If you want to play with and test CG models, then do a large systematic test (many systems). If the CG models perform reasonably, you have cleared everyone's conscience and will get a lot of citations. If they don't then you should try to understand why not. Are there fundamental flaws in the model? If so, can they be fixed? Have fun. What I mean by qualitatively is that I wouldn't trust a force-extension curve of such simulations (unless you do some force-matching :)) - re: FD144), but the conformational changes that are observed in a moderate pulling regime do seem to make sense. The experiments we carried out were interactive pulling experiments, either to induce opening and closure of the guanylate kinase enzyme or to explore the membrane anchoring and the mechanical properties of the SNARE complex. This is briefly described in reference [1]. Cheers, Marc [1] http://dx.doi.org/10.1002/jcc.21235 O. Delalande, N. Férey, G. Grasseau and M. Baaden: Complex Molecular Assemblies at hand via Interactive Simulations, 2009, J. Comp. Chem. x.peri...@rug.nl said: Hi Johnny, I am not familiar with pulling and even less with gromacs but I would be very cautious in using the MARTINI force field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested in knowing how it actually perform. XAvier. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pulling a CG protein
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote: Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these models have never been parameterized or systematically tested with this kind of application in mind. In general models that have been parameterized for one specific observable may not reproduce other observables *unless* the observables used for parameterization have a clear physical basis *and* the energy function captures the correct physics. Most biomolecular force fields (including Martini as far as I know) have been parameterized to reproduce density and energy of condensed phase (liquids), and hence this kind of data is usually reproduced quite well. However mixtures of components (e.g. two liquids) are usually not reproduced as well. By doing the kind of pulling simulations, preferably both atomistic and with CG models, one can try to verify whether the CG models can actually reproduce force curves to a comparable accuracy as all atom models. This kind of work should be done *systematically* before any applications. What does this boil down to? If you want to apply MD tools to get an accurate force curve *now*, use all atom models. If you want to play with and test CG models, then do a large systematic test (many systems). If the CG models perform reasonably, you have cleared everyone's conscience and will get a lot of citations. If they don't then you should try to understand why not. Are there fundamental flaws in the model? If so, can they be fixed? This is of course the idea, but then comes the problem of believing that atomistic simulations are actually giving the right answer! Have fun. What I mean by qualitatively is that I wouldn't trust a force- extension curve of such simulations (unless you do some force-matching :)) - re: FD144), but the conformational changes that are observed in a moderate pulling regime do seem to make sense. The experiments we carried out were interactive pulling experiments, either to induce opening and closure of the guanylate kinase enzyme or to explore the membrane anchoring and the mechanical properties of the SNARE complex. This is briefly described in reference [1]. Cheers, Marc [1] http://dx.doi.org/10.1002/jcc.21235 O. Delalande, N. Férey, G. Grasseau and M. Baaden: Complex Molecular Assemblies at hand via Interactive Simulations, 2009, J. Comp. Chem. x.peri...@rug.nl said: Hi Johnny, I am not familiar with pulling and even less with gromacs but I would be very cautious in using the MARTINI force field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested in knowing how it actually perform. XAvier. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pulling a CG protein
XAvier Periole wrote: On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote: Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these models have never been parameterized or systematically tested with this kind of application in mind. In general models that have been parameterized for one specific observable may not reproduce other observables *unless* the observables used for parameterization have a clear physical basis *and* the energy function captures the correct physics. Most biomolecular force fields (including Martini as far as I know) have been parameterized to reproduce density and energy of condensed phase (liquids), and hence this kind of data is usually reproduced quite well. However mixtures of components (e.g. two liquids) are usually not reproduced as well. By doing the kind of pulling simulations, preferably both atomistic and with CG models, one can try to verify whether the CG models can actually reproduce force curves to a comparable accuracy as all atom models. This kind of work should be done *systematically* before any applications. What does this boil down to? If you want to apply MD tools to get an accurate force curve *now*, use all atom models. If you want to play with and test CG models, then do a large systematic test (many systems). If the CG models perform reasonably, you have cleared everyone's conscience and will get a lot of citations. If they don't then you should try to understand why not. Are there fundamental flaws in the model? If so, can they be fixed? This is of course the idea, but then comes the problem of believing that atomistic simulations are actually giving the right answer! Of course, on the other hand CG models were developed to a large extent by comparison with A models, so if these are wrong, CG models are hopeless... In addition, especially for this kind of applications, does the experimental data measure the same thing that we try to calculate? Questions, questions. Have fun. What I mean by qualitatively is that I wouldn't trust a force-extension curve of such simulations (unless you do some force-matching :)) - re: FD144), but the conformational changes that are observed in a moderate pulling regime do seem to make sense. The experiments we carried out were interactive pulling experiments, either to induce opening and closure of the guanylate kinase enzyme or to explore the membrane anchoring and the mechanical properties of the SNARE complex. This is briefly described in reference [1]. Cheers, Marc [1] http://dx.doi.org/10.1002/jcc.21235 O. Delalande, N. Férey, G. Grasseau and M. Baaden: Complex Molecular Assemblies at hand via Interactive Simulations, 2009, J. Comp. Chem. x.peri...@rug.nl said: Hi Johnny, I am not familiar with pulling and even less with gromacs but I would be very cautious in using the MARTINI force field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested in knowing how it actually perform. XAvier. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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
Re: [gmx-users] Pulling a CG protein
On Jul 30, 2009, at 12:10 PM, David van der Spoel wrote: XAvier Periole wrote: On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote: Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these models have never been parameterized or systematically tested with this kind of application in mind. In general models that have been parameterized for one specific observable may not reproduce other observables *unless* the observables used for parameterization have a clear physical basis *and* the energy function captures the correct physics. Most biomolecular force fields (including Martini as far as I know) have been parameterized to reproduce density and energy of condensed phase (liquids), and hence this kind of data is usually reproduced quite well. However mixtures of components (e.g. two liquids) are usually not reproduced as well. By doing the kind of pulling simulations, preferably both atomistic and with CG models, one can try to verify whether the CG models can actually reproduce force curves to a comparable accuracy as all atom models. This kind of work should be done *systematically* before any applications. What does this boil down to? If you want to apply MD tools to get an accurate force curve *now*, use all atom models. If you want to play with and test CG models, then do a large systematic test (many systems). If the CG models perform reasonably, you have cleared everyone's conscience and will get a lot of citations. If they don't then you should try to understand why not. Are there fundamental flaws in the model? If so, can they be fixed? This is of course the idea, but then comes the problem of believing that atomistic simulations are actually giving the right answer! Of course, on the other hand CG models were developed to a large extent by comparison with A models, Yes on data from A models that were compared to Exp data, so as much reliable as possible :)) so if these are wrong, CG models are hopeless... Well now we use CG to (re)parameterize AT models ... just kidding ... In addition, especially for this kind of applications, does the experimental data measure the same thing that we try to calculate? Questions, questions. Have fun. What I mean by qualitatively is that I wouldn't trust a force- extension curve of such simulations (unless you do some force-matching :)) - re: FD144), but the conformational changes that are observed in a moderate pulling regime do seem to make sense. The experiments we carried out were interactive pulling experiments, either to induce opening and closure of the guanylate kinase enzyme or to explore the membrane anchoring and the mechanical properties of the SNARE complex. This is briefly described in reference [1]. Cheers, Marc [1] http://dx.doi.org/10.1002/jcc.21235 O. Delalande, N. Férey, G. Grasseau and M. Baaden: Complex Molecular Assemblies at hand via Interactive Simulations, 2009, J. Comp. Chem. x.peri...@rug.nl said: Hi Johnny, I am not familiar with pulling and even less with gromacs but I would be very cautious in using the MARTINI force field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested in knowing how it actually perform. XAvier. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Pulling a CG protein
Hi, Just picking up the following bits of the conversation: David van der Spoel wrote: What does this boil down to? If you want to apply MD tools to get an accurate force curve *now*, use all atom models. [..] x.peri...@rug.nl said: This is of course the idea, but then comes the problem of believing that atomistic simulations are actually giving the right answer! I think this is actually quite a valid point. As David pointed out, many forcefields have been parameterized with respect to density and energy data. So there is actually no guarantee that atomistic forcefields do particularly well with respect to pulling simulations (although many people have used them for such simulations). The gold standard should probably be to compare CG pull simulations directly to corresponding experimental data whenever possible. So have even more fun :) Marc -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pulling a CG protein
Hi XAvier, Marc, and David, Thank you so much for the reply and encouragement ;-). Please forgive me as I am trying to learn how to reply to the thread that I started. With regards to the fun discussion, it was my original intent to compare the results of pulling with the MARTINI forcefield (if the pull code was correct) with already published works on MD (using all-atomistic modeling of course :-)). I just wanted to know whether the pull code that I am using will be valid at all. If you guys can verify that would be awesome! Otherwise, I'd be happy to share the results with you guys if you wish. Again, thanks! --Johnny - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Pulling a CG protein
Dear gromacs users, Hi, I am trying to pull apart a relatively large protein (CG using the martini force field) by pulling on two groups in opposite directions. To do this, I will be using the following .mdp file. However, I am almost certain that it contains errors: title= Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 17000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 2500 nstvout = 2500 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; MARTINI - no need for more frequent updates ; or larger neighborlist cut-off due ; to the use of shifted potential energy functions. ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; MARTINI - vdw and electrostatic interactions are used ; in their shifted forms. Changing to other types of ; electrostatics will affect the general performance of ; the model. ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; MARTINI - normal temperature and pressure coupling schemes ; can be used. It is recommended to couple individual groups ; in your system seperately. ; Temperature coupling = tcoupl = V-Rescale ; Groups to couple separately = tc-grps = PROTEIN W ; Time constant (ps) and reference temperature (K) = tau_t= 0.3 0.3 ref_t= 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 3.0 compressibility = 3e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 323 gen_seed = 666 ; OPTIONS FOR BONDS = ; MARTINI - for ring systems constraints are defined ; which are best handled using Lincs. constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 60 ; FREEZE GROUP ; Pulling pull= afm pull_geometry = direction pull_start = no pull_nstxout= 10 pull_nstfout= 10 pull_ngroups= 2 pull_group0 = pull_group1 = pull pull_vec1 = -0.1764 -0.9823 -0.0625 pull_init1 = -0.1764 -0.9823 -0.0625 pull_rate1 = 0.0001 pull_k1 = 1000 pull_group2 = freeze pull_vec2 = 0.1764 0.9823 0.0625 pull_init2 = 0.1764 0.9823 0.0625 pull_rate2 = 0.01 pull_k2 = 5000 The reason why group 2 has such a high force constant and low pull rate is because I wanted to simulate putting a harmonic constraint on the freeze group. However, when I process this .mdp with grompp, I get the following message: WARNING 1 [file md_vinculin.mdp, line unknown]: Unknown or double left-hand 'pull_group2' in parameter file WARNING 2 [file md_vinculin.mdp, line unknown]: Unknown or double
