Re: [gmx-users] The water model with tip5p in gromos96
主月 ：） wrote: Hi everyone: I found that in tip5p.itp, there is a note tell user to use tip5p model with opls force field. But what i really want to use is the gromos96. How can i include tip5p model? copy the vanderwaals parameters for the TIP5P oxygen to the ffG43a1nb.itp file. Thanks a lot * Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ，82618423 * ___ 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 -- 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] Problem with trjconv centering after fitting
[EMAIL PROTECTED] wrote: Starting from a rhombic dodecahedron xtc file, trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless, a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why is this? ___ 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 could this be the same problem as reported here: http://bugzilla.gromacs.org/show_bug.cgi?id=99 -- 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
[gmx-users] tip4p or 5p
I want to build a water cell with 4p or 5p.How can i realized it? May be after include *.itp in current top, something need to be modified? It was said that 4p or 5p need OPLS together. How can i used it in GROMOS 96 *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ 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
[gmx-users] free energy
Dear all, Can I get the free energy during the conformation change of a protein using GROMACS3.1.4? And how? Regards Zhili___ 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
[gmx-users] remd ... is it exchanging?
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 -- 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? 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] Configuration on an IBM power computer
Volker Knecht wrote: Dear all, Hi Volker, cannot compute sizeof (int). one of us (Steffen Wolf, he's on this list, too) had this problem recently. It was solved by following these instructions: http://jumpdoc.fz-juelich.de/ibmsc/usage/FAQ/configure.html I have contacted Xie Yinghong who told me that this problem only occurs with the parallel and not with the sequential version. Yes, only the parallel version was affected. Hope that helped Christian ___ 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
[gmx-users] which vdwradii in pqr coming from editconf -mead ??
Dear community, I am producing pqr files with editconf -mead (starting from tpr files) in order to process them with apbs. The charges are the same as those of my topology, but I can't figure out from where the van der Waals radii are coming: -They don't match the ones I found in the file share/gromacs/top/vdwradii.dat -They don't match the ones I compute starting with the C6 and C12 coefficients of the LJ potentials. I compute them with eps=(C12/C6)^(1/6). Thank you very much for any hint! Pascal *** Pascal Baillod (PhD student) *** Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322 Institute of Chemical Sciences and Engineering ,Fax: +41-(0)21-693-0320 Laboratory of Computational Chemistry and Biochemistry [EMAIL PROTECTED] Room BCH 4121, Avenue Forel,http://lcbcpc21.epfl.ch CH-1015 Lausanne *** ___ 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
[gmx-users] Req for computer config for windows to run gromacs
Dear all, We are proposing to buy 5 computers, PC machines going to be used for general purpose as well as for running gromacs. The OS would be windowsXP. It would be more useful if you can suggest me some good configuration for this purpose. We are also planning cluster those PC for gromacs. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ 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
