Re: [gmx-users] Free energy landscape by g_sham
g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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] Free energy landscape by g_sham
Thank you Sir Regards kavya On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote: g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Making composite box in gromacs
I have polymer and clay structures and I need to study their surface interaction. How do I keep a clay box on top of polymer. 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] Free energy landscape by g_sham
On 2013-03-31 12:21, Kavyashree M wrote: Thank you Sir Note that the free energy differences are rigorously correct only if the array of the cells in the grid correspond units of phase space with the same volume. This is close to impossible to achieve, but the plots may still give insight. Regards kavya On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote: g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/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] Making composite box in gromacs
On 3/31/13 6:38 AM, Abhinav Agrawal wrote: I have polymer and clay structures and I need to study their surface interaction. How do I keep a clay box on top of polymer. The concepts of top and bottom are irrelevant in a periodic system. You can position anything within the unit cell wherever you like with editconf -center. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Inactivate position restraint
Hi, To inactivate a position restraint, is it enough to make the define command in mdp file to a comment? ;define= DPOSRES Sincerely, Shima -- 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] Inactivate position restraint
On 3/31/13 8:16 AM, Shima Arasteh wrote: Hi, To inactivate a position restraint, is it enough to make the define command in mdp file to a comment? ;define= DPOSRES Yes. Or remove it altogether. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] density profile
Dear all, In order to get density profile of a pure system the box has to get extended in one drection (e.g Z) as we do for surface tension calculations or density profile can be also obtained from the usual box filled up with the molecules without need for empty space in Z Thanks for any comments and advise in advance :) Best E. -- 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] density profile
On 3/31/13 11:41 AM, Elisabeth wrote: Dear all, In order to get density profile of a pure system the box has to get extended in one drection (e.g Z) as we do for surface tension calculations or density profile can be also obtained from the usual box filled up with the molecules without need for empty space in Z Thanks for any comments and advise in advance :) The density of the system is written to the .edr file. There is no need (or use) for a density profile if the system is homogeneous. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Structure file for di atmoic molecule
Dear gmx users, Does anyone know how to obtain structure file for the simple ethylene molecule ( C-C) ? I tried PRODRG but it fails to generate structure files for di atomic molecules. Any suggestion is appreciated! -- Thanks, J. N. -- 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] Structure file for di atmoic molecule
On 3/31/13 12:23 PM, Juliette N. wrote: Dear gmx users, Does anyone know how to obtain structure file for the simple ethylene molecule ( C-C) ? I tried PRODRG but it fails to generate structure files for di atomic molecules. Any suggestion is appreciated! For something as simple as a diatomic molecule, open up your favorite text editor and write it by hand :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] density profile
Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether running g_density on the current simulations cells provides the profile I am after. Do you have any clue whether or not the cell has to be extended in one direction to obtain the density profile? Thanks! On 31 March 2013 12:21, Justin Lemkul jalem...@vt.edu wrote: On 3/31/13 11:41 AM, Elisabeth wrote: Dear all, In order to get density profile of a pure system the box has to get extended in one drection (e.g Z) as we do for surface tension calculations or density profile can be also obtained from the usual box filled up with the molecules without need for empty space in Z Thanks for any comments and advise in advance :) The density of the system is written to the .edr file. There is no need (or use) for a density profile if the system is homogeneous. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] density profile
On 3/31/13 12:27 PM, Elisabeth wrote: Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether running g_density on the current simulations cells provides the profile I am after. Do you have any clue whether or not the cell has to be extended in one direction to obtain the density profile? If you're trying to produce an air-water interface, then indeed you will need some model for air within the unit cell, but there are several practical problems with that. The first is that g_density does not deal well with changing box vectors, and the density profiles it produces under an NPT ensemble are incorrect (outstanding bug that needs to be fixed, IIRC). The second is that if you run a simulation under NPT with void space, the unit cell will just compress down until there is no empty space. Probably the best solution would be to equilibrate under NPT at the desired conditions, then build a new unit cell and run under NVT. Using NVT will circumvent both problems, and if the proper pressure, density, etc have already been achieved, then you've got what you're after. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] density profile
Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v My questions are: 1) Can I get the proper solvent-air interface to obtain density profile by extending the Z direction (last line of the gro file obtained from NPT at each pressure)? Is that what yo mean by then build a new unit cell and run under NVT ? 2) Is the semi isotropic option with 0 compressibility in Z is appropriate to keep the pressure fixed? (as shown below in mdp settings)? 3) If the answer to q 2 is negative, whats is appropriate way to shift from NPt to NVT run. Do I have to use the equilibrated density from NPT runs and edit the last line of gro from -c flag of NPT.gro to obtain the correct density? The reason I am asking is that since P fluctuations are huge I am not sure if the the density of box from last frame of -c NPT.gro output is the correct density... Please advise on the above queries..Thanks a lot Below is the md.mdp contents: pbc = xyz integrator = md dt = 0.001 nsteps = 2000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100;1 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = Shift vdw-type= Shift rcoulomb-switch = 1 rvdw-switch = 1 ;0.9 ; Cut-offs rlist = 1.35 rcoulomb= 1.1 ;1.1 rvdw= 1.1 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 425 * * *Pcoupl = berendsen* *Pcoupltype = semiisotropic * *tau_p = 1 0.5* *compressibility = 3.5e-5 0* *ref_p = 50 ** * gen_vel = no gen_temp= 500.0 gen_seed= 173529 constraints = none constraint-algorithm = lincs On 31 March 2013 12:47, Justin Lemkul jalem...@vt.edu wrote: On 3/31/13 12:27 PM, Elisabeth wrote: Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether running g_density on the current simulations cells provides the profile I am after. Do you have any clue whether or not the cell has to be extended in one direction to obtain the density profile? If you're trying to produce an air-water interface, then indeed you will need some model for air within the unit cell, but there are several practical problems with that. The first is that g_density does not deal well with changing box vectors, and the density profiles it produces under an NPT ensemble are incorrect (outstanding bug that needs to be fixed, IIRC). The second is that if you run a simulation under NPT with void space, the unit cell will just compress down until there is no empty space. Probably the best solution would be to equilibrate under NPT at the desired conditions, then build a new unit cell and run under NVT. Using NVT will circumvent both problems, and if the proper pressure, density, etc have already been achieved, then you've got what you're after. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] density profile
On 3/31/13 1:12 PM, Elisabeth wrote: Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v My questions are: 1) Can I get the proper solvent-air interface to obtain density profile by extending the Z direction (last line of the gro file obtained from NPT at each pressure)? Is that what yo mean by then build a new unit cell and run under NVT ? That's one approach. It's not NVT if you're using pressure coupling, though. I would also be careful about using the term air here - if it's empty space, it's actually vacuum. 2) Is the semi isotropic option with 0 compressibility in Z is appropriate to keep the pressure fixed? (as shown below in mdp settings)? That should work. As long as the dimension along which you need the density profile is invariant, you should be able to circumvent any issues. -Justin 3) If the answer to q 2 is negative, whats is appropriate way to shift from NPt to NVT run. Do I have to use the equilibrated density from NPT runs and edit the last line of gro from -c flag of NPT.gro to obtain the correct density? The reason I am asking is that since P fluctuations are huge I am not sure if the the density of box from last frame of -c NPT.gro output is the correct density... Please advise on the above queries..Thanks a lot Below is the md.mdp contents: pbc = xyz integrator = md dt = 0.001 nsteps = 2000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100;1 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = Shift vdw-type= Shift rcoulomb-switch = 1 rvdw-switch = 1 ;0.9 ; Cut-offs rlist = 1.35 rcoulomb= 1.1 ;1.1 rvdw= 1.1 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 425 * * *Pcoupl = berendsen* *Pcoupltype = semiisotropic * *tau_p = 1 0.5* *compressibility = 3.5e-5 0* *ref_p = 50 ** * gen_vel = no gen_temp= 500.0 gen_seed= 173529 constraints = none constraint-algorithm = lincs On 31 March 2013 12:47, Justin Lemkul jalem...@vt.edu wrote: On 3/31/13 12:27 PM, Elisabeth wrote: Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether running g_density on the current simulations cells provides the profile I am after. Do you have any clue whether or not the cell has to be extended in one direction to obtain the density profile? If you're trying to produce an air-water interface, then indeed you will need some model for air within the unit cell, but there are several practical problems with that. The first is that g_density does not deal well with changing box vectors, and the density profiles it produces under an NPT ensemble are incorrect (outstanding bug that needs to be fixed, IIRC). The second is that if you run a simulation under NPT with void space, the unit cell will just compress down until there is no empty space. Probably the best solution would be to equilibrate under NPT at the desired conditions, then build a new unit cell and run under NVT. Using NVT will circumvent both problems, and if the proper pressure, density, etc have already been achieved, then you've got what you're after. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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
[gmx-users] Re: density profile
Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. You must use NVT only. Otherwise, the cell will compress in XY directions to compensate its inability to compress in Z direction. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v My questions are: 1) Can I get the proper solvent-air interface to obtain density profile by extending the Z direction (last line of the gro file obtained from NPT at each pressure)? Is that what yo mean by then build a new unit cell and run under NVT ? If you want solvent/air interface, you should add $air. If you want solvent/vacuum interface, it is enough to extend the box. If you want liquid/vapor interface, you need to re-equilibrate the system in NVT with a space for vapor available in the box. Dr. Vitaly Chaban -- 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: gmx-users Digest, Vol 107, Issue 133
Actually my doubt was how to make a simulation box from two structure files i.e. how do i keep the clay and poymer boxes close to each other to run energy minimization Message: 4 Date: Sun, 31 Mar 2013 07:38:38 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Making composite box in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5158203e.3020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/31/13 6:38 AM, Abhinav Agrawal wrote: I have polymer and clay structures and I need to study their surface interaction. How do I keep a clay box on top of polymer. The concepts of top and bottom are irrelevant in a periodic system. You can position anything within the unit cell wherever you like with editconf -center. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Making composite box in gromacs
On 3/31/13 2:22 PM, Abhinav Agrawal wrote: Actually my doubt was how to make a simulation box from two structure files i.e. how do i keep the clay and poymer boxes close to each other to run energy minimization Consider the following: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html The logic holds for any interfacial or inhomogeneous system. Place whatever species you want, wherever you want them in the box, with editconf -center, -translate, -rotate, etc as necessary. -Justin Message: 4 Date: Sun, 31 Mar 2013 07:38:38 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Making composite box in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5158203e.3020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/31/13 6:38 AM, Abhinav Agrawal wrote: I have polymer and clay structures and I need to study their surface interaction. How do I keep a clay box on top of polymer. The concepts of top and bottom are irrelevant in a periodic system. You can position anything within the unit cell wherever you like with editconf -center. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist 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: density profile
Thanks Vitaly. I am wondering what is the use of semiisotropic with 0 compressibility in Z then? I was hoping to run NPT to secure a fixed pressure. I also wanted to know if surface tension can be also calculated under NVT (if NPT fails for this puporse) Thanks! On 31 March 2013 14:01, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. You must use NVT only. Otherwise, the cell will compress in XY directions to compensate its inability to compress in Z direction. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v My questions are: 1) Can I get the proper solvent-air interface to obtain density profile by extending the Z direction (last line of the gro file obtained from NPT at each pressure)? Is that what yo mean by then build a new unit cell and run under NVT ? If you want solvent/air interface, you should add $air. If you want solvent/vacuum interface, it is enough to extend the box. If you want liquid/vapor interface, you need to re-equilibrate the system in NVT with a space for vapor available in the box. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
Hi Elisabeth - On Sun, Mar 31, 2013 at 8:28 PM, Elisabeth katesed...@gmail.com wrote: Thanks Vitaly. I am wondering what is the use of semiisotropic with 0 compressibility in Z then? I was hoping to run NPT to secure a fixed pressure. Please, read about Gibbs phase rule... This is your case. Anisotropic P-coupling is for certain tasks with anisotropic systems, i.e. where you have a large non-spherical object, such as nanotube or graphene. It is not for liquid/non-liquid interfaces. I also wanted to know if surface tension can be also calculated under NVT (if NPT fails for this puporse) I believe surface tension should be calculate ONLY from fixed-volume simulations. By definition of the property, isn't it? Thanks! Dr. Vitaly Chaban -- 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] Handy insertion of multiatomic particles
Dear All - Does Gromacs possess a convenient utility to [randomly] substitute solvent particles by given number of multiatomic solutes? Dr. Vitaly Chaban -- 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] Handy insertion of multiatomic particles
On 3/31/13 4:26 PM, Dr. Vitaly Chaban wrote: Dear All - Does Gromacs possess a convenient utility to [randomly] substitute solvent particles by given number of multiatomic solutes? No, but you can easily add the number of solutes you need with genbox -ci -nmol and then solvate afterwards. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Handy insertion of multiatomic particles
Yes, I can Could you briefly explain the difference between -cp and -cs options? On Sun, Mar 31, 2013 at 10:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/31/13 4:26 PM, Dr. Vitaly Chaban wrote: Dear All - Does Gromacs possess a convenient utility to [randomly] substitute solvent particles by given number of multiatomic solutes? No, but you can easily add the number of solutes you need with genbox -ci -nmol and then solvate afterwards. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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-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] Handy insertion of multiatomic particles
On 3/31/13 5:02 PM, Dr. Vitaly Chaban wrote: Yes, I can Could you briefly explain the difference between -cp and -cs options? From genbox -h: Specify -cp (solute) and -cs (solvent). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] g_cluster nan/segmentation fault error
Hi All, I'm trying to cluster a pdb trajectory format file and I'm getting odd results. The command line i'm using is: g_cluster -f 0to7.pdb -s cysTerm.pdb -g cluster.log -o rmsd-clust.xpm -dist rmsd-dist.xvg -cl clusters.pdb -method monte-carlo -seed 4540 -niter 1 And everything seems to go fine until the end, where it spits out the following set of results (input for fitting is C-Alpha, output C-Alpha): Reading frame 0 time -1.000'', 2038 atoms Reading frame1600 time 1599.000 Allocated 41086080 bytes for frames Read 1680 frames from trajectory 0to7.pdb Computing 1680x1680 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from -nan to -nan nm Average RMSD is -nan Number of structures for matrix 1680 Energy of the matrix is -nan nm Segmentation fault I don't honestly understand whats going on here, does anybody else have any ideas? Mark Ps. I'm pretty new to using the clustering utility. -- View this message in context: http://gromacs.5086.n6.nabble.com/g-cluster-nan-segmentation-fault-error-tp5006779.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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
[gmx-users] How to have two proteins randomly positioned and oriented in the box
Hi everyone, I am trying to insert two same proteins in a simulation box. Now I have used pdb2gmx to convert one protein's pdb file to gro file. Then how should I do? How could they be randomly positioned and oriented in the box? Thanks in advance. Zhikun -- 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 have two proteins randomly positioned and oriented in the box
On 3/31/13 9:51 PM, Zhikun Cai wrote: Hi everyone, I am trying to insert two same proteins in a simulation box. Now I have used pdb2gmx to convert one protein's pdb file to gro file. Then how should I do? How could they be randomly positioned and oriented in the box? Place them however you like within the box using editconf -center, -translate, -rotate, etc as necessary. You may be able to get completely random insertion with genbox -ci -nmol, but I've never tried it with a protein. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Glutamate to Alanine Mutation
Dear Prof Mobley, I have some additional questions in understanding the free energy calculations. 1) When doing a mutation from a larger aminoacid to a smaller one, one necessarily ends up with dummy atoms and atoms that have different mass. In my case when the glutamate is converted into a glycine or an alanine a carbon will become a hydrogen (change in mass) and the rest of the excess atoms will become dummies with the mass they had in Glu. The change in mass has an effect in the kinetic energy part of the Hamiltonian contribution to the free energy and this change is properly computed by Gromacs as dKe/dL. However it is clear from this procedure that because the dummies have mass, the mass of Ala or Gly will not be the correct and therefore dKe/dL would be quite meaningless. I read papers that suggest only integrating the potential energy component dV/dL. In fact for example, the Amber11 manual indicates that Amber mutations only change the potential but keep all masses the same as they were before the alchemical change. Clearly having dummies with no mass would fix this issue but it would be problematic because F=m*a and with m=0 for a given finite F, the acceleration on the dummies would be infinite. In Monte Carlo all of this is irrelevant because one only computes the potential contribution to the free energy difference but in MD the story is different. What is the customary approach to deal with this? Just use dV/dL and discard dKe/dL? 2) The g_bar analysis appears to assume that the interpolation between states a and b is linear (g_bar issues a warning using the derivative data (dH/dlambda) to extrapolate delta H values. This will only work if the Hamiltonian is linear in lambda. ). However when using softcore potentials lambda also enters in the expression for r. It would appear that the interpolation is not really linear even though the LJ transformation also looks like Va *lambda+ (1- lambda)* Vb Nonetheless I see g_bar being used for such transformations. Could you shed light on this? 3) Also it is common to use small lambda spacings (close to lambda=0 and lambda=1) but somewhat larger spacing between 0.1 and 0.9. How does g_bar handle this? Is the integration and error analysis done correctly even when the lambda spacing may be different at different lambda values? Thank you for your time. Regards Sai On Tue, Dec 4, 2012 at 5:27 PM, Sai Kumar Ramadugu sramad...@gmail.comwrote: Dear Prof Mobley, Thank you very much for your time. While I was waiting for your opinion on my topology files, I did several tests to see what happens. The tests I did are: 1. Mutate only the amino acid (Glutamate -1 charge) and no mutation of K+ ion, but have positional restraints on the ion. 2. Mutate only the amino acid (Glutamate -1 charge) and no mutation of K+ ion and no positional restraints or constraints on the system 3. The actual simulation that caused me trouble, ie with position restraints, constraints and mutating the ion concurrently. Finally I decided to use the simulation data from no restraints or constraints and no mutation of K+ ion. With this approach now I am getting a positive deldelG value for the mutation going from Glutamate to Alanine. On Mon, Dec 3, 2012 at 4:07 PM, David Mobley dmob...@gmail.com wrote: Hi, I had a look at your topologies and don't see anything obviously wrong. You may however want to check that none of the bonded parameters involving the transformed atoms are being unexpectedly perturbed. (In our setups we typically repeat the A state parameters in the B state column for the bonds, angles, and torsions, as some GROMACS versions would otherwise assume these should be turned to zero). I read in the gromacs manual that with opls_aa force field, the state A parameters are repeated if you dont have any parameters for state B. I saw those warnings issued by grompp and in order to avoid any problems I did repeat the state A parameters in state B columns as you do it. Sorry I can't be more help. I'm pretty swamped on this end. I once again, I thank you very much for the time you took for my problem. Regards Sai On Tue, Oct 30, 2012 at 10:35 AM, Sai Kumar Ramadugu sramad...@gmail.com wrote: Prof Mobley, I just want to add that in the topology file named Ala_charge_off.top, I am *turning off* the charges on atoms of alanine 40 residue. The total integral of dV/dl from 0 to 1 gave me a value of 274.73 kJ/mol and I took the negative of this as this should be same as *turning on* the charges. To justify my approach I did add the partial charges on Ala40 residue in a separate set of simulations (which finished today morning) and the total integral of dV/dl from 0 to 1 gave me a value of -274.705 kJ/mol. Regards Sai On Sat, Oct 27, 2012 at 11:00 AM, Sai Kumar Ramadugu sramad...@gmail.com wrote: Dear Prof Mobley, I have attached the topologies for all three steps in presence of ligand. The case
