Re: [gmx-users] UREA + Protein Simulation error.
Dear David, Thanks for the reply, guess i will do some literature survey and see if i can find some validated urea parameters. karan On Mon, Sep 21, 2009 at 8:51 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: karan syal wrote: Dear Justin, Thanks for the reply! I will surely try minimize the protein in Vacuum and then try adding Urea again. Just that i was wondering how will that effect my artifact bonds which are between Urea and Water, and not at all between any Protein atom and Urea/Sol?? As i mentioned earlier, these bonds are formed only after minimization, they are not present before adding 10M urea+water box (No such bonds in its individual 10M urea+water .gro either ) to protein, they are neither there in the before minimized protein+10M urea+water system. Don't use the Urea topology that is in the gromacs distribution. It is not based on any force field known to man. Thanks again, cherrz karan On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: karan syal wrote: Dear Gromacs users, I am trying to run a urea+protein simulation and encountering a few problems at various stages. I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K) I am using this equilibrated box to add to a globular protein of about 250 residues using following commands : editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron (Giving me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the number of urea above box should add is 2448.) genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro (*This adds 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M urea box i have solvated with??)* No, it shouldn't. The protein occupies space within that volume, as well. When i try to minimize this using the following em.mdp cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 5000 coulombtype = PME pme_order = 4 nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 *It gives me the following output* Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 5000 Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is larger than the 1-4 table size 2.000 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 t = 0.015 ps: Water molecule starting at atom 34477 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 100. Potential Energy = -1.3092671e+22 Maximum force =inf on atom 12598 Norm of force =inf gcq#160: The Microsecond is Within Reach (P.J. Van Maaren) /When i look at the file in VMD, the protein is completely out of the box + There are unusual bonds between a lot of UREA and SOL molecules/. ( The unusual bonds are artifcats after minimization which are not there when i initially look at my P48_10Mrea.gro, that is the gro generated after genbox wth -cs as 10M urea) Out of the box doesn't exist for a periodic system. The bonds you see are also *not* generated by Gromacs, but are also just an artefact of visualization. Bonds are not created or broken in molecular mechanics. I tried constraining hbonds as well in em.mdp bit to no effect. I used the above em.gro to run a production run, with following pr.mdp Don't, it's a waste of time.
Re: [gmx-users] UREA + Protein Simulation error.
karan syal wrote: Dear Gromacs users, I am trying to run a urea+protein simulation and encountering a few problems at various stages. I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K) I am using this equilibrated box to add to a globular protein of about 250 residues using following commands : editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron(Giving me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the number of urea above box should add is 2448.) genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro (*This adds 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M urea box i have solvated with??)* No, it shouldn't. The protein occupies space within that volume, as well. When i try to minimize this using the following em.mdp cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 5000 coulombtype = PME pme_order = 4 nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 *It gives me the following output* Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 5000 Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is larger than the 1-4 table size 2.000 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 t = 0.015 ps: Water molecule starting at atom 34477 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 100. Potential Energy = -1.3092671e+22 Maximum force =inf on atom 12598 Norm of force =inf gcq#160: The Microsecond is Within Reach (P.J. Van Maaren) /When i look at the file in VMD, the protein is completely out of the box + There are unusual bonds between a lot of UREA and SOL molecules/. ( The unusual bonds are artifcats after minimization which are not there when i initially look at my P48_10Mrea.gro, that is the gro generated after genbox wth -cs as 10M urea) Out of the box doesn't exist for a periodic system. The bonds you see are also *not* generated by Gromacs, but are also just an artefact of visualization. Bonds are not created or broken in molecular mechanics. I tried constraining hbonds as well in em.mdp bit to no effect. I used the above em.gro to run a production run, with following pr.mdp Don't, it's a waste of time. Never just plow ahead when something isn't working. There is something unreasonable about the starting structure. Try minimizing the protein in vacuo first, then add your urea and try EM again. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://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] UREA + Protein Simulation error.
Dear Justin, Thanks for the reply! I will surely try minimize the protein in Vacuum and then try adding Urea again. Just that i was wondering how will that effect my artifact bonds which are between Urea and Water, and not at all between any Protein atom and Urea/Sol?? As i mentioned earlier, these bonds are formed only after minimization, they are not present before adding 10M urea+water box (No such bonds in its individual 10M urea+water .gro either ) to protein, they are neither there in the before minimized protein+10M urea+water system. Thanks again, cherrz karan On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: karan syal wrote: Dear Gromacs users, I am trying to run a urea+protein simulation and encountering a few problems at various stages. I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K) I am using this equilibrated box to add to a globular protein of about 250 residues using following commands : editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron(Giving me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the number of urea above box should add is 2448.) genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro (*This adds 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M urea box i have solvated with??)* No, it shouldn't. The protein occupies space within that volume, as well. When i try to minimize this using the following em.mdp cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 5000 coulombtype = PME pme_order = 4 nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 *It gives me the following output* Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 5000 Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is larger than the 1-4 table size 2.000 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 t = 0.015 ps: Water molecule starting at atom 34477 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 100. Potential Energy = -1.3092671e+22 Maximum force =inf on atom 12598 Norm of force =inf gcq#160: The Microsecond is Within Reach (P.J. Van Maaren) /When i look at the file in VMD, the protein is completely out of the box + There are unusual bonds between a lot of UREA and SOL molecules/. ( The unusual bonds are artifcats after minimization which are not there when i initially look at my P48_10Mrea.gro, that is the gro generated after genbox wth -cs as 10M urea) Out of the box doesn't exist for a periodic system. The bonds you see are also *not* generated by Gromacs, but are also just an artefact of visualization. Bonds are not created or broken in molecular mechanics. I tried constraining hbonds as well in em.mdp bit to no effect. I used the above em.gro to run a production run, with following pr.mdp Don't, it's a waste of time. Never just plow ahead when something isn't working. There is something unreasonable about the starting structure. Try minimizing the protein in vacuo first, then add your urea and try EM again. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://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] UREA + Protein Simulation error.
karan syal wrote: Dear Justin, Thanks for the reply! I will surely try minimize the protein in Vacuum and then try adding Urea again. Just that i was wondering how will that effect my artifact bonds which are between Urea and Water, and not at all between any Protein atom and Urea/Sol?? As i mentioned earlier, these bonds are formed only after minimization, they are not present before adding 10M urea+water box (No such bonds in its individual 10M urea+water .gro either ) to protein, they are neither there in the before minimized protein+10M urea+water system. There are no bonds. Visualization software attempts to guess where bonds should be based on distances between atoms. The only bonds that are actually present are defined in the topology. It is impossible for bonds to break and form in a standard MD or EM protocol - it defies the physics! -Justin Thanks again, cherrz karan On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: karan syal wrote: Dear Gromacs users, I am trying to run a urea+protein simulation and encountering a few problems at various stages. I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K) I am using this equilibrated box to add to a globular protein of about 250 residues using following commands : editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron (Giving me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the number of urea above box should add is 2448.) genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro (*This adds 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M urea box i have solvated with??)* No, it shouldn't. The protein occupies space within that volume, as well. When i try to minimize this using the following em.mdp cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 5000 coulombtype = PME pme_order = 4 nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 *It gives me the following output* Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 5000 Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is larger than the 1-4 table size 2.000 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 t = 0.015 ps: Water molecule starting at atom 34477 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 100. Potential Energy = -1.3092671e+22 Maximum force =inf on atom 12598 Norm of force =inf gcq#160: The Microsecond is Within Reach (P.J. Van Maaren) /When i look at the file in VMD, the protein is completely out of the box + There are unusual bonds between a lot of UREA and SOL molecules/. ( The unusual bonds are artifcats after minimization which are not there when i initially look at my P48_10Mrea.gro, that is the gro generated after genbox wth -cs as 10M urea) Out of the box doesn't exist for a periodic system. The bonds you see are also *not* generated by Gromacs, but are also just an artefact of visualization. Bonds are not created or broken in molecular mechanics. I tried constraining hbonds as well in em.mdp bit to no effect. I used the above em.gro to run a production run, with following pr.mdp Don't, it's a waste of time. Never just
Re: [gmx-users] UREA + Protein Simulation error.
karan syal wrote: Dear Justin, Thanks for the reply! I will surely try minimize the protein in Vacuum and then try adding Urea again. Just that i was wondering how will that effect my artifact bonds which are between Urea and Water, and not at all between any Protein atom and Urea/Sol?? As i mentioned earlier, these bonds are formed only after minimization, they are not present before adding 10M urea+water box (No such bonds in its individual 10M urea+water .gro either ) to protein, they are neither there in the before minimized protein+10M urea+water system. Don't use the Urea topology that is in the gromacs distribution. It is not based on any force field known to man. Thanks again, cherrz karan On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: karan syal wrote: Dear Gromacs users, I am trying to run a urea+protein simulation and encountering a few problems at various stages. I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K) I am using this equilibrated box to add to a globular protein of about 250 residues using following commands : editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron (Giving me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the number of urea above box should add is 2448.) genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro (*This adds 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M urea box i have solvated with??)* No, it shouldn't. The protein occupies space within that volume, as well. When i try to minimize this using the following em.mdp cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 5000 coulombtype = PME pme_order = 4 nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 *It gives me the following output* Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 5000 Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is larger than the 1-4 table size 2.000 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 t = 0.015 ps: Water molecule starting at atom 34477 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 100. Potential Energy = -1.3092671e+22 Maximum force =inf on atom 12598 Norm of force =inf gcq#160: The Microsecond is Within Reach (P.J. Van Maaren) /When i look at the file in VMD, the protein is completely out of the box + There are unusual bonds between a lot of UREA and SOL molecules/. ( The unusual bonds are artifcats after minimization which are not there when i initially look at my P48_10Mrea.gro, that is the gro generated after genbox wth -cs as 10M urea) Out of the box doesn't exist for a periodic system. The bonds you see are also *not* generated by Gromacs, but are also just an artefact of visualization. Bonds are not created or broken in molecular mechanics. I tried constraining hbonds as well in em.mdp bit to no effect. I used the above em.gro to run a production run, with following pr.mdp Don't, it's a waste of time. Never just plow ahead when something isn't working. There is something unreasonable about the starting structure. Try minimizing the protein in vacuo first, then add your urea and try EM again.
