Re: [gmx-users] Req for computer config for windows to run gromacs
raja wrote: 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 Run Linux on them. It will save you a lot of problems... Otherwise you're on your own. -- 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] which vdwradii in pqr coming from editconf -mead ??
[EMAIL PROTECTED] wrote: 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! there are different options: -rvdw real 0.12 Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file -sig56 real 0 Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 -[no]vdwread bool no Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field Default is to compute them from the lennard jones parameters. Note that if you want to reproduce literature data you need to use their charges and radii. By the way, we have tried some calculations with MEAD, but find that the results are chaotic. An infinitesimal change in coordinates will give very large variations in energy, and there is no convergence to a certain energy if one makes the grid spacing smaller either. Is that a generic feature of these kind of programs? Is it better in APBS? -- 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] 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
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] 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] 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
Re: [gmx-users] Problem with trjconv centering after fitting
Thanks Tsjerk, that works great! Also your explaination was very clear. I would just like to follow up that what works for me was (2 steps): trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans I now understand also why the following single step conversion doesn't work, but perhaps this following combination should be disallowed by trjconv or the code should be changed to do the rotation as the last step: trjconv -s a.tpr -f a.xtc -o c.xtc -center tric -ur compact -fit rot+trans -pbc inbox > From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Problem with trjconv centering after fitting > To: "Discussion list for GROMACS users" > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > Would that be the same? What happened here is that the system was > first fitted. Thus, the system is rotated and any operation concerning > pbc after that point will be screwed up, because the box definition > does not match the system. Solution: first perform all operations > involving pbc, then fit the system. Note that translations are not a > problem, only rotations. An alternative solution would be to have all > routines involving rotation of the frame also rotating the box > definition in that frame in the trajectory. But this requires > modifications in many routines. > > Tsjerk > > On 8/28/06, David van der Spoel <[EMAIL PROTECTED]> wrote: > > [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 > > > > > -- > > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > > > -- > > ___ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 28, Issue 81 > * > ___ 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, I have a problem with the configuration of gmx3.3 on an IBM power computer which was reported in here in the mailing list previously by Xie Yinghong. When trying to configure a parallel version of gmx on an IBM power computer with operating system AIX, I recieve the error "cannot compute sizeof (int)". I have contacted Xie Yinghong who told me that this problem only occurs with the parallel and not with the sequential version. He could not solve the problem, but, rather, uses gmx3.2 now for which the problem does not occur. This is, however, no option for me, as I want to use a feature not implemented in gmx3.2 yet. Does anyone have any idea how to solve this problem? Your help would be greatly appreciated. Kind regards, Volker Since you're at a Max Planck address I'd suggest you contact the staff at the Rechenzentrum in Garching, they have been involved in some GROMACS developments as well and they know the machine. -- 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?
Carsten Baldauf wrote: 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? In fact we had very (too) little water, and were we to do the simulations again we would use more. When your peptide collapses in solvent it will be smaller, but at high T it may still be slightly extended. I'd suggest doing a short test sim at high T (but not higher than the boiling point...) to see how large you need to take the box. I'd also suggest not using higher than 373 K, at least if you want to interpret the data at high T as well. If you want to use REMD solely for sampling at lower T you can use unphysically T as well (unphysical because the water does not evaporate at T > 373 in the simulation). -- 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] Configuration on an IBM power computer
Hi, Volker I have installed Gromacs 3.3.1 on a couple of IBM power computers (i.e. P655+). You need to install fftw3, and not fftw 2.15. fftw 2.15 didn't seem to work with AIX 5.2. Here are the instructions: Installing fftw3 setenv MPICC 'mpcc_r -q64' setenv CC 'xlc_r -q64' setenv F77 'xlf_r -q64' setenv OBJECT_MODE 64 setenv LDFLAGS setenv CPPFLAGS setenv FFLAGS '-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 -qstrict' setenv CFLAGS '-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 -qstrict' ./configure --prefix=/rmount/users09/washu/aroberts/fftw3 --enable-float make make install Installing Gromacs 3.3.1 setenv MPICC 'mpcc_r -q64' setenv CC 'xlc_r -q64' setenv F77 'xlf_r -q64' setenv OBJECT_MODE 64 setenv FFLAGS '-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 -qstrict' setenv CFLAGS '-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 -qstrict -I/rmount/users09/washu/aroberts/fftw3/gromacs-3.3.1/include -I/usr/include' setenv LDFLAGS '-L/rmount/users09/washu/aroberts/fftw3/lib' setenv CPPFLAGS '-I/rmount/users09/washu/aroberts/fftw3/include' poe "./configure --enable-mpi --disable-vectorized-sqrt --program-suffix="_mpi" --prefix=/rmount/users09/washu/aroberts/gromacs_3.3.1s --exec-prefix=/rmount/users09/washu/aroberts/gromacs_3.3.1s" You may need to adjust this for your particular computer configuration, but I have gotten this to essentially work on two IBM Power P655+. I hope this helps. Best wishes, Art Roberts Department of Medicinal Chemistry University of Washington Seattle, WA 98195 --- Volker Knecht <[EMAIL PROTECTED]> wrote: > Dear all, > > I have a problem with the configuration of gmx3.3 on > an IBM power > computer which was reported in here in the mailing > list previously by > Xie Yinghong. When trying to configure a parallel > version of gmx on an > IBM power computer with operating system AIX, I > recieve the error > > "cannot compute sizeof (int)". > > I have contacted Xie Yinghong who told me that this > problem only occurs > with the parallel and not with the sequential > version. He could not > solve the problem, but, rather, uses gmx3.2 now for > which the problem > does not occur. This is, however, no option for me, > as I want to use a > feature not implemented in gmx3.2 yet. > > Does anyone have any idea how to solve this problem? > > Your help would be greatly appreciated. > > Kind regards, > Volker > > -- > Dr. Volker Knecht > Theory Department > Max Planck Institute of Colloids and Interfaces > Research Campus Golm > 14424 Potsdam, Germany > > Phone: +49-331-567-9610 > Fax: +49-331-567-9612 > > ___ > 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 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] Configuration on an IBM power computer
Dear all, I have a problem with the configuration of gmx3.3 on an IBM power computer which was reported in here in the mailing list previously by Xie Yinghong. When trying to configure a parallel version of gmx on an IBM power computer with operating system AIX, I recieve the error "cannot compute sizeof (int)". I have contacted Xie Yinghong who told me that this problem only occurs with the parallel and not with the sequential version. He could not solve the problem, but, rather, uses gmx3.2 now for which the problem does not occur. This is, however, no option for me, as I want to use a feature not implemented in gmx3.2 yet. Does anyone have any idea how to solve this problem? Your help would be greatly appreciated. Kind regards, Volker -- Dr. Volker Knecht Theory Department Max Planck Institute of Colloids and Interfaces Research Campus Golm 14424 Potsdam, Germany Phone: +49-331-567-9610 Fax: +49-331-567-9612 ___ 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 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?
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 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
[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] problems with energy minimization
Martin wrote: Dear all, I´m a beginner in the field of molecular dynamics and have just installed the gromacs software. I have problems with energy minimization. When trying out the md tutorial on the lysozyme structure 1AKI.pdb using the provided minim.mdp file the minimization finishes with the message: this is a FAQ, but the answer is, this result is fine as a start for MD simulation. Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up minim_traj.trr to ./#minim_traj.trr.4# Back Off! I just backed up confout.gro to ./#confout.gro.4# Steepest Descents converged to machine precision in 79 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.13948846313191e+04 Maximum force = 1.94715000386709e+03 on atom 1113 Norm of force = 8.53155624640669e+03 I already tried different minimization algorithms with different settings and also compiled the code with double precision accuracy without success. Thank you very much for any advice, Martin ___ 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
[gmx-users] problems with energy minimization
Dear all, I´m a beginner in the field of molecular dynamics and have just installed the gromacs software. I have problems with energy minimization. When trying out the md tutorial on the lysozyme structure 1AKI.pdb using the provided minim.mdp file the minimization finishes with the message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up minim_traj.trr to ./#minim_traj.trr.4# Back Off! I just backed up confout.gro to ./#confout.gro.4# Steepest Descents converged to machine precision in 79 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.13948846313191e+04 Maximum force = 1.94715000386709e+03 on atom 1113 Norm of force = 8.53155624640669e+03 I already tried different minimization algorithms with different settings and also compiled the code with double precision accuracy without success. Thank you very much for any advice, Martin ___ 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
Hi, Would that be the same? What happened here is that the system was first fitted. Thus, the system is rotated and any operation concerning pbc after that point will be screwed up, because the box definition does not match the system. Solution: first perform all operations involving pbc, then fit the system. Note that translations are not a problem, only rotations. An alternative solution would be to have all routines involving rotation of the frame also rotating the box definition in that frame in the trajectory. But this requires modifications in many routines. Tsjerk On 8/28/06, David van der Spoel <[EMAIL PROTECTED]> wrote: [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 -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ 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] 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
