[gmx-users] Re: P4_error for extending coarse grained MD simulations
Could anyone give me more suggestions? Many thanks! 2010/6/24 张春雷 chunleizhang@gmail.com Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I have searched the mail-list, but found no similar report. I also search through google, but no answer seems satisfactory. I once performed extending simulation for all atom simulation, and the method mentioned above worked. Is anyone familiar with MARTINI CG simulation? Could you give me some suggestions? Many thanks! 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
[gmx-users] g_msd and diffusion coefficent
Hi gromacs users I did simulation of pr-dna by gromacs. I want to obtain diffusion coefficent of pr to dna. I raed manual (g_msd) in which there are diffusion coefficent only for 1 and 2 dimension as follows respectively : -type : Compute diffusion coefficient in one direction: no, x, y or z -lateral : Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z how to use g_msd for calculation of diffusion coeffcient in 3D. Thanks a lot in advance. -- 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
[gmx-users] Re: Diffusion constant
Dear Teobaldo, I think your calculation should be as easy as: g_msd -n index.ndx where index.ndx contains the atom numbers belonging to that one molecule in water. Good luck, Vitaly Dear Users I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way: Obtaining a continuos trajectory 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc Obtaining the msd of the solute, removing the center of mass of the system Firt way: 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm I choose SOLUTE Second way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv I choose SOLUTE There are significative differences in the results? according to the gromacs manual -mv option is used in molecules, What is the correct step, 2a or 2b? Regards Teobaldo -- 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] g_anaeig -proj
Hi Chris, Carla, Sorry I didn't reply before. To understand the projections, first consider the following. Take a single atom with three coordinates (x,y,z). These coordinates are the projections onto a set of (three, Cartesian) axes. If you consider, e.g., the projection of the coordinates onto the x-axis, you're left with a single number in distance measure (nm in gromacs). Now let's say your coordinates are (1,1,1). If you then take the axis (x+y+z), rather than one of the original ones, and project your coordinates onto it, you get a projection of sqrt(3) nm. To describe all of Cartesian space, you need two more axes, orthogonal to x+y+z, but for this particular point the projections will both be zero. Now for a complete configuration, it's a bit more complicated. You best think of it as a point in 3N-dimensional space, having specific projections or scores on 3N mutually orthogonal axes. These projections still have the same units (nm). The aim of PCA is to find new axes in this space that better describe a distribution of these points, i.e. a set of configurations. Each configuration has one projection on each axis. If you only select one eigenvector, the projection will give a single number. Filtering is the next step. If you have a projection of a configuration onto a selected number of components, you can consider that as having the projections on all other axes set to zero. In other words, the variance or noise associated with these other axes is removed. If you project these projections back to the original space, then you've effectively filtered out the variance/noise. I hope that clarifies a bit. ### Tsjerk: First, great tutorial, I hadn't seen this before. Second, you might avoid this type of confusion by mentioning during the command: Thnx :) g_anaeig -s ../topol.tpr -f ../traj.xtc -v eigenvectors.trr -eig eigenvalues.xvg -proj proj-ev1.xvg -extr ev1.pdb -rmsf rmsf-ev1.xvg -first 1 -last 1 that you care actually doing a few things at once... or perhaps actually break the command apart into separate g_anaeig -proj and g_anaeig -extr calls. ### Agreed. It's probably best to have the different operations split. All: might it be a good idea to get the html addresses of nice tutorials into the output messages of the analysis tools? That would only make sense if the tutorials are adopted and put on the gromacs site. Otherwise the tutorials/sites are probably too volatile. Adoption raises questions regarding responsibility and maintenance though. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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
[gmx-users] B-factor
Hi all excuse me for my past incomplete email. I want to calculate B-factor using g_rmsf command as follows: g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq this command give me a pdb file whereas I want to obtain text file (numeral value of B-factor ). how to obtain B-factor value from this pdb file? any help will highly appreciated. -- 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] B-factor
shahab shariati skrev: Hi all excuse me for my past incomplete email. I want to calculate B-factor using g_rmsf command as follows: g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq this command give me a pdb file whereas I want to obtain text file (numeral value of B-factor ). how to obtain B-factor value from this pdb file? any help will highly appreciated. Look in the b-factor field. See the reference for the pdb file format. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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
[gmx-users] B-factor
Hi all I want to calculate B-factor using g_rmsf command as follows g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq -- 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
[gmx-users] the job is not being distributed
hello, I am running a simulation on dual core processor using the following command mpirun -np 8 mdrun_mpi -s top The job is running but it is not distributed on other node, i mean i cant see the process on other nodes as well. I see only on node01 but it has only 4 processors. Can anybody suggest me! -- 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] the job is not being distributed
On Jun 28, 2010, at 2:34 PM, Syed Tarique Moin wrote: hello, I am running a simulation on dual core processor using the following command mpirun -np 8 mdrun_mpi -s top The job is running but it is not distributed on other node, i mean i cant see the process on other nodes as well. I see only on node01 but it has only 4 processors. Can anybody suggest me! Hi, find out how you generally run a simple parallel job with the MPI framework that you are using. If that works, Gromacs should also run in parallel. You are going to have to provide some kind of machine / host / nodefile. Carsten -- 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
[gmx-users] B-factor
Dear *Erik Marklund* what do you meant from See the reference for the pdb file format? is b-factor a file? please guide me more. I am beginner in gromacs. -- 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] B-factor
shahab shariati skrev: Dear *Erik Marklund* what do you meant from See the reference for the pdb file format? is b-factor a file? please guide me more. I am beginner in gromacs. Hi, A pdb file can store many things other than atomic coordinates, for instance b-factors. The pdb-format is not a gromacs invention however, and its documentation for the pdb-format can be found at www.pdb.org -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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] g_msd and diffusion coefficent
leila karami wrote: Hi gromacs users I did simulation of pr-dna by gromacs. I want to obtain diffusion coefficent of pr to dna. I raed manual (g_msd) in which there are diffusion coefficent only for 1 and 2 dimension as follows respectively : -type : Compute diffusion coefficient in one direction: no, x, y or z -lateral : Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z how to use g_msd for calculation of diffusion coeffcient in 3D. Do not use either of these flags. -Justin Thanks a lot in advance. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] Re: g_msd and diffusion coefficent
Very easy. Just forget about those options: g_msd Vitaly Hi gromacs users I did simulation of pr-dna by gromacs. I want to obtain diffusion coefficent of pr to dna. I raed manual (g_msd) in which there are diffusion coefficent only for 1 and 2 dimension as follows respectively : -type : Compute diffusion coefficient in one direction: no, x, y or z -lateral : Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z how to use g_msd for calculation of diffusion coeffcient in 3D. Thanks a lot in advance. -- 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
[gmx-users] RE: Diffusion constant
Dear Vitaly Your answer is equivalente to the 2a option of my firts e-mail. Will you explain me the meaning of the -mv option.?, why not use -mv in my command line? There are bit differences between the 2a and 2b option, whic is the correct? Regards Ricardo .. Date: Mon, 28 Jun 2010 13:26:33 +0300 Subject: Re: Diffusion constant From: vvcha...@gmail.com To: gmx-users@gromacs.org CC: rcu...@hotmail.com Dear Teobaldo, I think your calculation should be as easy as: g_msd -n index.ndx where index.ndx contains the atom numbers belonging to that one molecule in water. Good luck, Vitaly Dear Users I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way: Obtaining a continuos trajectory 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc Obtaining the msd of the solute, removing the center of mass of the system Firt way: 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm I choose SOLUTE Second way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv I choose SOLUTE There are significative differences in the results? according to the gromacs manual -mv option is used in molecules, What is the correct step, 2a or 2b? Regards Teobaldo _ Regardez-moi dans les yeux : vidéobavardage GRATUIT http://go.microsoft.com/?linkid=9734396-- 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] RE: Diffusion constant
Ricardo Cuya Guizado wrote: Dear Vitaly Your answer is equivalente to the 2a option of my firts e-mail. Will you explain me the meaning of the -mv option.?, why not use -mv in my command line? There are bit differences between the 2a and 2b option, whic is the correct? No, your two commands are identical. The -mw option is set to yes by default, so in essence, 2a actually uses -mw as well. The -mol option plots MSD per molecule, perhaps that's what you're referring to? -Justin Regards Ricardo .. Date : Mon, 28 Jun 2010 13:26:33 +0300 Subject: Re: Diffusion constant From: vvcha...@gmail.com To: gmx-users@gromacs.org CC: rcu...@hotmail.com Dear Teobaldo, I think your calculation should be as easy as: g_msd -n index.ndx where index.ndx contains the atom numbers belonging to that one molecule in water. Good luck, Vitaly Dear Users I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way: Obtaining a continuos trajectory 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc Obtaining the msd of the solute, removing the center of mass of the system Firt way: 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm I choose SOLUTE Second way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv I choose SOLUTE There are significative differences in the results? according to the gromacs manual -mv option is used in molecules, What is the correct step, 2a or 2b? Regards Teobaldo Jeux Messenger : mettez vos amis au défi! Jeux Messenger! http://go.microsoft.com/?linkid=9734391 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] the job is not being distributed
Hi, In case Amber simulation, i run command of mpirun and the jobs are distributed into different nodes 4 on each machines but in case i am observing that all the 8 processes are on node01 but no indication on node02 unlike in case of amber. Thanks Syed Tarique Moin -- 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] the job is not being distributed
So which MPI library are you using? Carsten On Jun 28, 2010, at 3:33 PM, Syed Tarique Moin wrote: Hi, In case Amber simulation, i run command of mpirun and the jobs are distributed into different nodes 4 on each machines but in case i am observing that all the 8 processes are on node01 but no indication on node02 unlike in case of amber. Thanks Syed Tarique Moin -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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
[gmx-users] Re: Diffusion constant
Ricardo, Hmm... My g_msd (4.0.7) doesn't not have -mv option. Do you mean mass-weighted (MW) constant here? If you want to get the classical diffusion constant, it is mass-weighted by definition. Vitaly On Mon, Jun 28, 2010 at 4:18 PM, Ricardo Cuya Guizado rcu...@hotmail.com wrote: Dear Vitaly Your answer is equivalente to the 2a option of my firts e-mail. Will you explain me the meaning of the -mv option.?, why not use -mv in my command line? There are bit differences between the 2a and 2b option, whic is the correct? Regards Ricardo .. Date : Mon, 28 Jun 2010 13:26:33 +0300 Subject: Re: Diffusion constant From: vvcha...@gmail.com To: gmx-users@gromacs.org CC: rcu...@hotmail.com Dear Teobaldo, I think your calculation should be as easy as: g_msd -n index.ndx where index.ndx contains the atom numbers belonging to that one molecule in water. Good luck, Vitaly Dear Users I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way: Obtaining a continuos trajectory 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc Obtaining the msd of the solute, removing the center of mass of the system Firt way: 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm I choose SOLUTE Second way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv I choose SOLUTE There are significative differences in the results? according to the gromacs manual -mv option is used in molecules, What is the correct step, 2a or 2b? Regards Teobaldo Jeux Messenger : mettez vos amis au défi! Jeux Messenger! -- 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
[gmx-users] RE: Diffusion constant
Dears Justin and Vitaly I make a mistake in my firts e-mail the option is not -mv is -mol as Justin mentioned So the second step was: Obtaining the msd of the solute, removing the center of mass of thesystem Firts way:2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcommI choose SOLUTESecond way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mol I choose SOLUTE In the two cases the solute was choose , the differences in the solute Cont. Diffusion is in one order of magnitude. What is the correct step for calculate the Dif. const , 2a or 2b? Regars Ricardo _ MSN Rencontres: Faites une rencontre spéciale cette année. http://go.microsoft.com/?linkid=9734394-- 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
[gmx-users] Re: Diffusion constant
Ricardo, -mol is for each molecule separately. So averaging among (identical) molecules will not be performed. As I suppose this is for the different debug runs mostly. To get the ordinary diffusion constant just g_msd is enough. To get the diffusion constant of any specific group of atoms, use NDX file and type the atom numbers there. Good luck, Vitaly On Mon, Jun 28, 2010 at 8:22 PM, Ricardo Cuya Guizado rcu...@hotmail.com wrote: Dears Justin and Vitaly I make a mistake in my firts e-mail the option is not -mv is -mol as Justin mentioned So the second step was: Obtaining the msd of the solute, removing the center of mass of the system Firts way: 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm I choose SOLUTE Second way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mol I choose SOLUTE In the two cases the solute was choose , the differences in the solute Cont. Diffusion is in one order of magnitude. What is the correct step for calculate the Dif. const , 2a or 2b? Regars Ricardo Courez la chance de voir la photo de votre coin de pays sur Bing.ca Soumettez une photo maintenant! -- 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] CL atom not being recognised
jayant james wrote: Hi! The protein I am attempting to simulate has a CL atom. When I run pdb2gmx I get the following error message. Any help in overcoming this problem would be appreciated. Thanks James -- Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms while sorting atoms --- You haven't told us which force field you're trying to use, but I'm guessing that the chloride .rtp entry is probably named CL instead of CL- (which is used by the ffG* force fields). You can check the .rtp file to be sure. Also, I would strongly suggest upgrading to version 4.0.7 - there have been numerous bug fixes and performance upgrades since version 4.0. -Justin -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] Re: gromacs with CMAP
Hi, all I recently download the git version and test the CMAP. However, very strange result I get. I want to use CMAP support in my own coarse-grained force field. Basically, I construct a ALA-ALA-ALA system and turn off all energy terms except bond length, bond angle and CMAP to do some test. The CMAP is only applied to phi,psi of central residue with a constant value of -5 (unit is kj/mol, right?) on a 24*24 grid. The result Rama plot is not a uniformed distribution as expected but avoid 27 regular distributed region ! (Sorry I can't attach a figure due to size limit). Can someone help me out? best dawei -- 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] CL atom not being recognised
Hi! I am using the gromos9643a1 forcefield and the chloride is described as given below in the rtp file. I have described the CL as CL- in my pdb input file and still it is not accepting! I am using V 4.0.5 [ CL- ] [ atoms ] CL CL--1.0 0 [ bonds ] [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type On Mon, Jun 28, 2010 at 4:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Hi! The protein I am attempting to simulate has a CL atom. When I run pdb2gmx I get the following error message. Any help in overcoming this problem would be appreciated. Thanks James -- Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms while sorting atoms --- You haven't told us which force field you're trying to use, but I'm guessing that the chloride .rtp entry is probably named CL instead of CL- (which is used by the ffG* force fields). You can check the .rtp file to be sure. Also, I would strongly suggest upgrading to version 4.0.7 - there have been numerous bug fixes and performance upgrades since version 4.0. -Justin -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- 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
[gmx-users] No convergence in Diffusion Coefficient
See the table bellow, there is no convergence of the Self-Diffusion Coefficient (Dself) over the trajectory length. Dself is obtained for NPT box of 1024 SPC/E water molecules by the Einstein's relation (via RMSD). In Gromacs Manual or AlienTildesley's book I didn't find issues related to the problem. Is there any idea why I can not achieve the convergence? Description: To figure out what the trajectory length is needed for an accurate simulation of the self-diffusion coefficient I performed the following test. Split the continuous 10ns long trajectory on parts and calculated Dself for each of the parts, e.g. the splitting on N parts gives N values of Dself obtained on trjlenth=10ns/N trajectory part. For the variety of N values we can calculate the average Dself and dispersion Disper. The converged trajectory length is found as the trjlenth value at which the dispersion is sufficiently small and Dself equal to the value obtained for the whole 10ns trajectory. But it turned out that Dself does not converge (See the columns 3 and 4 in the Table). Just for the comparison I carried out the same test for the Dielectric Constant Eps (See the columns 5 and 6 in the Table) and the converged trajectory length is about 2.5-5ns which correlates with the length reported in the literature. trjlenth N Dself Disper Eps Disper ps 1e-5 cm^2/s 1.0 1 2.63050 72.0 0 5000.0 2 2.4591.0929 71.9 1.1 2500.0 4 2.4554.0291 71.6 4.7 1250.0 8 2.4816.0618 71.1 5.2 625.0 16 2.4848.0786 70.6 7.5 312.5 32 2.4993.0848 67.7 9.4 156.2 64 2.5128.1082 63.311.6 78.1 128 2.4993.1119 56.314.1 39.0 256 2.5072.1303 43.614.9 19.5 512 2.5133.1713 31.012.4 9.7 1030 2.5449.2128 19.6 8.0 4.8 2083 2.6318.2373 12.0 4.9 -- 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] Re: gromacs with CMAP
On 2010-06-29 03.48, Da-Wei Li wrote: Hi, all I recently download the git version and test the CMAP. However, very strange result I get. I want to use CMAP support in my own coarse-grained force field. Basically, I construct a ALA-ALA-ALA system and turn off all energy terms except bond length, bond angle and CMAP to do some test. The CMAP is only applied to phi,psi of central residue with a constant value of -5 (unit is kj/mol, right?) on a 24*24 grid. The result Rama plot is not a uniformed distribution as expected but avoid 27 regular distributed region ! (Sorry I can't attach a figure due to size limit). Can someone help me out? Maybe the angle potential also implicitly imposes limits to the phi/psi available space? Try turning it off. best dawei -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] No convergence in Diffusion Coefficient
On 2010-06-29 05.50, Igor Leontyev wrote: See the table bellow, there is no convergence of the Self-Diffusion Coefficient (Dself) over the trajectory length. Dself is obtained for NPT box of 1024 SPC/E water molecules by the Einstein's relation (via RMSD). In Gromacs Manual or AlienTildesley's book I didn't find issues related to the problem. Is there any idea why I can not achieve the convergence? Description: To figure out what the trajectory length is needed for an accurate simulation of the self-diffusion coefficient I performed the following test. Split the continuous 10ns long trajectory on parts and calculated Dself for each of the parts, e.g. the splitting on N parts gives N values of Dself obtained on trjlenth=10ns/N trajectory part. For the variety of N values we can calculate the average Dself and dispersion Disper. The converged trajectory length is found as the trjlenth value at which the dispersion is sufficiently small and Dself equal to the value obtained for the whole 10ns trajectory. But it turned out that Dself does not converge (See the columns 3 and 4 in the Table). Just for the comparison I carried out the same test for the Dielectric Constant Eps (See the columns 5 and 6 in the Table) and the converged trajectory length is about 2.5-5ns which correlates with the length reported in the literature. You don't say how you compute the Dself. Your Dself varies from 2.48 to 2.63, and if you drop the 10 ns and 4.8 ps measurements it varies from 2.48 to 2.54. Not too much I would say. g_msd tries to do something semi-intelligent, by fitting the MSD to a straight line from 10 to 90% of the length of the graph. You should avoid using the very first few ps and the final bit of the graph. Another way of getting statistics is by spitting the system in 2-N sub-boxes and computing the Dself for each of these. trjlenth N Dself Disper Eps Disper ps 1e-5 cm^2/s 1.0 1 2.6305 0 72.0 0 5000.0 2 2.4591 .0929 71.9 1.1 2500.0 4 2.4554 .0291 71.6 4.7 1250.0 8 2.4816 .0618 71.1 5.2 625.0 16 2.4848 .0786 70.6 7.5 312.5 32 2.4993 .0848 67.7 9.4 156.2 64 2.5128 .1082 63.3 11.6 78.1 128 2.4993 .1119 56.3 14.1 39.0 256 2.5072 .1303 43.6 14.9 19.5 512 2.5133 .1713 31.0 12.4 9.7 1030 2.5449 .2128 19.6 8.0 4.8 2083 2.6318 .2373 12.0 4.9 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
[gmx-users] B-factor
Dear Erik Marklund thanks for your attention I saw www.pdb.org. there is b-factor in pdb files being in this website but pdb file obtained form g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq command, has not B-factor. my bfac.pdb file is as follows : TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 62.008 62.008 62.008 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00272.65 ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 ATOM 23 CA SER 3 25.254 48.487 33.290 1.00189.09 ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00114.27 ATOM 41 CA SER 5 27.814 48.657 27.860 1.00195.51 ATOM 52 CA SER 6 31.164 48.167 26.020 1.00217.99 ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00300.70 ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00248.64 ATOM 92 CA GLY 9 35.314 45.957 18.630 1.00184.40 ATOM 99 CA GLY 10 37.064 42.607 19.150 1.00139.99 ATOM 106 CA GLN 11 37.224 39.007 17.810 1.00106.39 ATOM 123 CA VAL 12 34.754 36.657 19.540 1.00 78.29 ATOM 139 CA ARG 13 33.244 33.847 17.550 1.00 79.41 ATOM 163 CA PHE 14 32.044 30.277 17.980 1.00 23.96 ATOM 183 CA SER 15 30.254 27.737 15.740 1.00 44.68 ATOM 194 CA ASN 16 26.794 26.277 16.430 1.00 54.17 ATOM 208 CA ASP 17 28.154 23.097 18.090 1.00 52.38 ATOM 220 CA GLN 18 30.914 24.937 19.880 1.00 25.27 ATOM 237 CA THR 19 28.404 27.377 21.340 1.00 24.72 ATOM 251 CA ILE 20 26.264 24.487 22.620 1.00 35.92 ATOM 270 CA GLU 21 29.004 22.497 24.430 1.00 22.96 ATOM 285 CA LEU 22 30.324 25.797 25.950 1.00 13.17 ATOM 304 CA GLU 23 26.874 26.467 27.560 1.00 26.01 ATOM 319 CA LYP 24 26.474 22.877 28.710 1.00 37.38 ATOM 341 CA LYP 25 29.944 22.657 30.270 1.00 29.72 ATOM 363 CA PHE 26 29.484 26.037 32.040 1.00 33.01 ATOM 383 CA GLU 27 26.304 24.837 33.730 1.00 56.55 ATOM 398 CA THR 28 28.194 21.907 35.400 1.00 71.22 ATOM 412 CA GLN 29 31.264 24.057 36.290 1.00 61.11 ATOM 429 CA LYP 30 31.314 27.927 35.980 1.00 53.89 ATOM 451 CA TYR 31 35.124 27.747 35.600 1.00 54.07 ATOM 472 CA LEU 32 37.594 25.107 34.310 1.00 52.72 ATOM 491 CA SER 33 40.974 24.187 35.600 1.00 49.43 ATOM 510 CA PRO 34 43.864 24.147 33.110 1.00 41.67 ATOM 524 CA PRO 35 44.074 20.337 32.590 1.00 46.11 ATOM 530 CA GLU 36 40.404 20.317 31.650 1.00 30.32 ATOM 545 CA ARG 37 40.464 23.597 29.640 1.00 17.05 ATOM 569 CA LYP 38 43.434 22.497 27.460 1.00 19.61 ATOM 591 CA ARG 39 41.524 19.337 26.310 1.00 21.22 ATOM 615 CA LEU 40 38.184 21.167 25.940 1.00 10.93 ATOM 634 CA ALA 41 39.834 23.657 23.510 1.00 10.81 ATOM 644 CA LYP 42 41.344 20.617 21.670 1.00 20.84 ATOM 666 CA MET 43 38.004 18.787 21.490 1.00 19.62 ATOM 683 CA LEU 44 35.884 21.877 20.620 1.00 16.95 ATOM 702 CA GLN 45 38.504 23.247 18.140 1.00 23.14 ATOM 719 CA LEU 46 38.814 26.507 20.170 1.00 17.31 ATOM 738 CA SER 47 41.784 28.247 21.770 1.00 22.52 ATOM 749 CA GLU 48 42.464 28.237 25.540 1.00 18.67 ATOM 764 CA ARG 49 41.984 32.017 25.510 1.00 22.59 ATOM 788 CA GLN 50 38.484 31.627 24.050 1.00 17.42 ATOM 805 CA VAL 51 37.614 28.917 26.620 1.00 8.87 ATOM 821 CA LYP 52 38.664 31.067 29.630 1.00 15.01 ATOM 843 CA THR 53 37.104 34.267 28.220 1.00 21.29 ATOM 857 CA TRP 54 33.794 32.697 27.320 1.00 15.97 ATOM 881 CA PHE 55 33.164 31.167 30.720 1.00 16.56 ATOM 901 CA GLN 56 34.244 34.267 32.580 1.00 27.30 ATOM 918 CA ASN 57 31.854 36.577 30.640 1.00 31.82 ATOM 932 CA ARG 58 29.204 33.887 30.940 1.00 28.78 ATOM 956 CA ARG 59 29.414 34.027 34.740 1.00 42.57 ATOM 980 CA ALA 60 28.834 37.777 34.520 1.00 52.64 ATOM 990 CA LYP 61 25.674 36.957 32.590 1.00 47.32 ATOM 1012 CA TRP 62 24.714 34.207 35.090 1.00109.93 ATOM 1036 CA ARG 63 25.094 36.337 38.210 1.00145.64 ATOM 1060 CA ARG 64 22.154 38.367 36.850 1.00409.17 ATOM 1084 CA SER 65 19.994 35.337 36.560 1.00567.55 ATOM 1095 CA GLY 66 20.044 34.427 40.200 1.00313.57 ATOM 1110 CA PRO 67 22.124 34.867 43.420 1.00232.72 ATOM 1116 CA SER 68 22.484 31.017 43.640 1.00296.77 ATOM 1127 CA SER 69 26.064 29.747 43.910 1.00746.26 ATOM 1138 CA CGL 70 26.794 26.717 41.750 1.001312.96 TER ENDMDL -- 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
