Re: [gmx-users] remd ... is it exchanging?
Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 residue peptide using 16 replicas in a temperature range from 275 to 419 kelvin. i follow the method described here: Seibert, M., Patriksson, A., Hess, B., van der Spoel, D. Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 354:173–183, 2005. when i look in the *log files is think i find the sections logging the exchanges: Replica exchange at step 1000 time 2 Repl 0 - 1 dE = 3.180e+01 dpV = 5.043e-04 d = 3.180e+01 Repl ex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Repl pr .00 .00 .00 .00 .00 .00 .00 .00 the line 'Repl pr ' allways only contains .00's. thus i guess there is no exchange happening. am i right? what are the possible reasons and what you suggest me to change? thanks a lot// carsten yes. in the Seibert paper the number of atoms was very small 4000. The number of replicas should be inversely proportional to the number of atoms, so if you have 16000 atoms you need 64 replicas to cover this T-range. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] remd ... is it exchanging?
dear david// i never used pymol ... in your paper you write you solvated using pymol. is it a plugin or or a standard feature? can you give me a hint how to do it? thanks// carsten David van der Spoel wrote: Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 residue peptide using 16 replicas in a temperature range from 275 to 419 kelvin. i follow the method described here: Seibert, M., Patriksson, A., Hess, B., van der Spoel, D. Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 354:173–183, 2005. when i look in the *log files is think i find the sections logging the exchanges: Replica exchange at step 1000 time 2 Repl 0 - 1 dE = 3.180e+01 dpV = 5.043e-04 d = 3.180e+01 Repl ex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Repl pr .00 .00 .00 .00 .00 .00 .00 .00 the line 'Repl pr ' allways only contains .00's. thus i guess there is no exchange happening. am i right? what are the possible reasons and what you suggest me to change? thanks a lot// carsten yes. in the Seibert paper the number of atoms was very small 4000. The number of replicas should be inversely proportional to the number of atoms, so if you have 16000 atoms you need 64 replicas to cover this T-range. -- dr carsten baldauf biotechnologisches zentrum der tu dresden http://www.biotec.tu-dresden.de/pisabarro http://www.biotec.tu-dresden.de/~carstenb Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html No Software Patents! See http://www.ffii.org/index.en.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] remd ... is it exchanging?
Carsten Baldauf wrote: dear david// i never used pymol ... in your paper you write you solvated using pymol. is it a plugin or or a standard feature? can you give me a hint how to do it? It doesn't write that... We used pymol (pymol.sf.net) to generate the starting structure of our peptide. Genbox was used for solvation. thanks// carsten David van der Spoel wrote: Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 residue peptide using 16 replicas in a temperature range from 275 to 419 kelvin. i follow the method described here: Seibert, M., Patriksson, A., Hess, B., van der Spoel, D. Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 354:173–183, 2005. when i look in the *log files is think i find the sections logging the exchanges: Replica exchange at step 1000 time 2 Repl 0 - 1 dE = 3.180e+01 dpV = 5.043e-04 d = 3.180e+01 Repl ex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Repl pr .00 .00 .00 .00 .00 .00 .00 .00 the line 'Repl pr ' allways only contains .00's. thus i guess there is no exchange happening. am i right? what are the possible reasons and what you suggest me to change? thanks a lot// carsten yes. in the Seibert paper the number of atoms was very small 4000. The number of replicas should be inversely proportional to the number of atoms, so if you have 16000 atoms you need 64 replicas to cover this T-range. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] remd ... is it exchanging?
ok, i got it wrong ... i see now my problem ... i am using an extremely big box ... the length of my fully extended peptide is about 5.6 nm i will try a box with an image distance of 5.7 nm. this should more or less resemble the status of your input, am i right? thanks for the help// carsten David van der Spoel wrote: Carsten Baldauf wrote: dear david// i never used pymol ... in your paper you write you solvated using pymol. is it a plugin or or a standard feature? can you give me a hint how to do it? It doesn't write that... We used pymol (pymol.sf.net) to generate the starting structure of our peptide. Genbox was used for solvation. thanks// carsten David van der Spoel wrote: Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 residue peptide using 16 replicas in a temperature range from 275 to 419 kelvin. i follow the method described here: Seibert, M., Patriksson, A., Hess, B., van der Spoel, D. Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 354:173–183, 2005. when i look in the *log files is think i find the sections logging the exchanges: Replica exchange at step 1000 time 2 Repl 0 - 1 dE = 3.180e+01 dpV = 5.043e-04 d = 3.180e+01 Repl ex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Repl pr .00 .00 .00 .00 .00 .00 .00 .00 the line 'Repl pr ' allways only contains .00's. thus i guess there is no exchange happening. am i right? what are the possible reasons and what you suggest me to change? thanks a lot// carsten yes. in the Seibert paper the number of atoms was very small 4000. The number of replicas should be inversely proportional to the number of atoms, so if you have 16000 atoms you need 64 replicas to cover this T-range. -- dr carsten baldauf biotechnologisches zentrum der tu dresden http://www.biotec.tu-dresden.de/pisabarro http://www.biotec.tu-dresden.de/~carstenb Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html No Software Patents! See http://www.ffii.org/index.en.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] remd ... is it exchanging?
Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 residue peptide using 16 replicas in a temperature range from 275 to 419 kelvin. i follow the method described here: Seibert, M., Patriksson, A., Hess, B., van der Spoel, D. Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 354:173–183, 2005. when i look in the *log files is think i find the sections logging the exchanges: Replica exchange at step 1000 time 2 Repl 0 - 1 dE = 3.180e+01 dpV = 5.043e-04 d = 3.180e+01 Repl ex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Repl pr .00 .00 .00 .00 .00 .00 .00 .00 the line 'Repl pr ' allways only contains .00's. thus i guess there is no exchange happening. am i right? Yep. You will see x between pairs of numbers in the Repl ex line when exchange occured successfully between those pairs. You can experiment with making your temperature gaps smaller to get a feel for how close they need to be for your size of system. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
