[gmx-users] simulated annealing mdp
Hi Gromacs Friends, I planed to do simulated annealing... My protocol is as follow ( forcefield G96 53a6 spc water model) 1. nvt at 310 k for 100 ps 2. Sa (mdp is posted below ) 3. NPT at 310 k for 100 ps Is it right ?? Please suggest me improvements... Sa mdp file title= gromacs define= -DPOSRES; position restrain the protein nstcomm= 1 comm-mode= Linear; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 0.2 ps nstvout= 1000; save velocities every 0.2 ps nstenergy= 1000; save energies every 0.2 ps nstlog= 1000; update log file every 0.2 ps ; Bond parameters continuation= yes; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 0.9; short-range neighborlist cutoff (in nm) rcoulomb= 0.9; short-range electrostatic cutoff (in nm) vdw-type= Cut-off rvdw= 1.4; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 310 310; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off ; Simulated annealing annealing = single single annealing_npoints= 4 4 annealing_time = 0 200 400 600 0 200 400 600 annealing_temp = 310 323 300 310 310 323 300 310 Thank you in advance With Best Wishes, Rama David -- 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] simulated annealing mdp
On 6/12/12 3:39 AM, rama david wrote: Hi Gromacs Friends, I planed to do simulated annealing... My protocol is as follow ( forcefield G96 53a6 spc water model) 1. nvt at 310 k for 100 ps 2. Sa (mdp is posted below ) 3. NPT at 310 k for 100 ps Is it right ?? There are two levels of right - suitability of purpose and syntactic correctness. The latter is easily solved by running grompp. If there's a problem, you'll know in five seconds rather than waiting a few hours for help. With respect to the former, you should decide on a protocol based on established procedures and the goals of your study. There are many questions you should ask yourself. What do you hope to achieve using the SA protocol shown? How will it aid your study? Should you use a wider range of temperatures for any particular reason? From what I see, you've got a protein in water and you're restraining the protein. The SA protocol simply heats and cools water, which I don't think accomplishes much. -Justin Please suggest me improvements... Sa mdp file title= gromacs define= -DPOSRES; position restrain the protein nstcomm= 1 comm-mode= Linear; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 0.2 ps nstvout= 1000; save velocities every 0.2 ps nstenergy= 1000; save energies every 0.2 ps nstlog= 1000; update log file every 0.2 ps ; Bond parameters continuation= yes; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 0.9; short-range neighborlist cutoff (in nm) rcoulomb= 0.9; short-range electrostatic cutoff (in nm) vdw-type= Cut-off rvdw= 1.4; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 310 310; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off ; Simulated annealing annealing = single single annealing_npoints= 4 4 annealing_time = 0 200 400 600 0 200 400 600 annealing_temp = 310 323 300 310 310 323 300 310 Thank you in advance With Best Wishes, Rama David -- 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] simulated annealing mdp
THANK YOU 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] simulated annealing mdp
On Tue, Jun 12, 2012 at 4:42 PM, rama david ramadavidgr...@gmail.comwrote: THANK YOU 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 Hello Justin, In the last message you said SA protocol simply heats and cools water, which I don't think accomplishes much.. can you suggest the other paramaters that must be used achieve, lets say the proper folding of loops in a GPCR. Secondly.,,In temperature coupling he used 310 for the non protein system and a range of temeratures from 310-323-310 for simulated aneealing.. how the program treats the couling temperatures and annealing temperatures (310 and 310-323-310).. Can you explain what temperature is applied to what groups in simple membrane system with a GPCR system.. ; Temperature coupling is on tc-grps= Protein Non-Protein; two coupling groups - more accurate ref_t= 310 310; reference temperature, one for each group, in K ;sim anealing annealing_time = 0 200 400 600 0 200 400 600 annealing_temp = 310 323 300 310 310 323 300 310 . '(Sorry if it feels like a premature question.. But I'm a beginner ) Thanks -- Virus -- 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] simulated annealing mdp
On 6/12/12 8:20 AM, Lord RaviRaj .. wrote: On Tue, Jun 12, 2012 at 4:42 PM, rama david ramadavidgr...@gmail.com mailto:ramadavidgr...@gmail.com wrote: THANK YOU Justin, -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Hello Justin, In the last message you said SA protocol simply heats and cools water, which I don't think accomplishes much.. can you suggest the other paramaters that must be used achieve, lets say the proper folding of loops in a GPCR. I should clarify that - the SA protocol does indeed heat and cool the protein as well, but accomplishes nothing because restraints were applied. To refine loops, don't use restraints. One can create a custom posre.itp file with genrestr to restrain some parts of a protein (i.e., well-folded secondary structure elements) while letting others move. This may be necessary if using high temperatures that would otherwise cause the protein to unfold. Restraints can be useful, if applied appropriately. Secondly.,,In temperature coupling he used 310 for the non protein system and a range of temeratures from 310-323-310 for simulated aneealing.. how the program treats the couling temperatures and annealing temperatures (310 and 310-323-310).. Can you explain what temperature is applied to what groups in simple membrane system with a GPCR system.. Temperatures are scaled linearly between the values listed in annealing_temp over the times set in annealing_time. The values set for ref_t are irrelevant, but one does need to set appropriate values for other temperature coupling parameters. -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] simulated annealing mdp
Hello Justin and Ravi, Lets explain me Why I did simulated anealing?? .. I synthesise peptide and I have experimental data for its self assembly, I just want to reproduced these data. I arranged the 32 protein in axis to petide fibre, in antiparrallel Beta sheet structure. I dont have crystal structure , Thats why I did SA in the hope that after these the side chain may be get properly oriented with respect to each other.That will give me good structure for production run. I also run system withought SA , but I get good result by following SA protocol. In posrestrain only backbone is restrained and the sidechain is free to move, So I think it may be help to achieve my goal. After these I also plan to use SA as production run, then compare the result with previous protocols. Please give valuable suggestion to improve my study protocol.. With Best Wishes, Rama David. -- 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] simulated annealing mdp
On 6/12/12 9:09 AM, rama david wrote: Hello Justin and Ravi, Lets explain me Why I did simulated anealing?? .. I synthesise peptide and I have experimental data for its self assembly, I just want to reproduced these data. I arranged the 32 protein in axis to petide fibre, in antiparrallel Beta sheet structure. I dont have crystal structure , Thats why I did SA in the hope that after these the side chain may be get properly oriented with respect to each other.That will give me good structure for production run. I also run system withought SA , but I get good result by following SA protocol. In posrestrain only backbone is restrained and the sidechain is free to move, So I think it may be help to achieve my goal. After these I also plan to use SA as production run, then compare the result with previous protocols. Please give valuable suggestion to improve my study protocol.. Seems reasonable. Stating this up front in the original message would have saved some time. Otherwise, we make assumptions ;) -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] simulated annealing mdp
Thank you for reply -- 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
