[gmx-users] wrong string length 0 for string buf
Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o com.xtc -pbc nojump -ur compact -center gromacs gives me the following error: Program trjconv, VERSION 4.0.5 Source code file: gmxfio.c, line: 609 Fatal error: wrong string length 0 for string buf (source tpxio.c, line 1641) Any suggestions would be greatly 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] wrong string length 0 for string buf
Hi, Your tpr file is probably empty (0 bytes). Berk Date: Sat, 21 Aug 2010 11:54:17 +0330 From: karami.lei...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] wrong string length 0 for string buf Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o com.xtc -pbc nojump -ur compact -center gromacs gives me the following error: Program trjconv, VERSION 4.0.5 Source code file: gmxfio.c, line: 609 Fatal error: wrong string length 0 for string buf (source tpxio.c, line 1641) Any suggestions would be greatly 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 -- 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] How to do Energy minimization and MD of protein-new ligand complex
I am new to Gromacs. I have a protein where ligand is bound to it. I got this complex after carrying out docking of ligand to protein.The ligand is new. So no topology and parameter files are available. At first i want to carryout energy minimization of this complex and then I want to find out how ligand interacts with the protein active site residue by carrying a MD simulation. So can anyone guide me how to proceed. It would be a great help Thanks -- 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] How to do Energy minimization and MD of protein-new ligand complex
priyabrata panigrahi wrote: I am new to Gromacs. I have a protein where ligand is bound to it. I got this complex after carrying out docking of ligand to protein.The ligand is new. So no topology and parameter files are available. At first i want to carryout energy minimization of this complex and then I want to find out how ligand interacts with the protein active site residue by carrying a MD simulation. So can anyone guide me how to proceed. It would be a great help Thanks http://www.gromacs.org/Documentation/Tutorials Of particular interest is the "GROMACS tutorial for drug - enzyme complex." But before you proceed with collecting your own data following this procedure, please see here: http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips -Justin -- 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] Calculate observed "Acceptance Ratio" from REMD simulation
Calculate observed "Acceptance Ratio" from REMD simulation Dear Gromacs users, I used the Gromacs how-to [1] to setup a REMD simulation. The targeted acceptance ratio was P_acp=15%, I used the temperature generator web-service [2] to get the temperature spacing. From the test simulation I want to calculate the observed acceptance ratio P_obs. The last md.log file gives a "Replica exchange statistic". I got following questions regarding on how to calculate P_obs. 1. To get P_obs from simulation I have to calculate the ratio between the successful exchange and total exchange attempts. Is this correct? I checked several papers and books (Frenkel/Smit, etc.), I only found the formula how to calculate the temperature spacing given P_acp. But I couldn't find a formula or definition how to calculate P_obs from a simulation. Is the above definition of P_obs correct? 2. The md.log file "Replica exchange statistic" gives in my case following summary [3]. For temperature T0 to T1 there wehre 664 successful exchanges. The number of exchange attempts were 1213. The ratio 664/1213 gives 55%. Would the P_obs=55% , is this correct? 3. A observed ratio of P_obs=50% given a targeted acceptance ratio of P_acp=15% is quite high. What can be the reason for this large discrepancy? 4. Could the Gromacs users, admin etc. please add some more information to the REMD Howto [1]. In particular regarding how to calculate P_obs? It would be a really useful for the Gromacs users. Can I as a Gromacs user add some more information to the howto or do I need a login? I would appreciate any help. Thanks, Henri 1: Replica-Exchange Molecular Dynamics howto http://www.gromacs.org/Documentation/How-tos/REMD 2: Temperature generator for REMD-simulations http://folding.bmc.uu.se/remd/ 3: "md.log" file summary Replica exchange statistics Repl 2425 attempts, 1213 odd, 1212 even Repl average probabilities: Repl 0123456789 10 ... Repl .55 .55 .55 .56 .56 .54 .56 .56 .56 .56 ... Repl number of exchanges: Repl 0123456789 10 ... Repl 664 684 667 692 659 627 699 688 699 683 ... Repl average number of exchanges: Repl 0123456789 10 ... Repl .55 .56 .55 .57 .54 .52 .58 .57 .58 .56 ... -- 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] Calculate observed "Acceptance Ratio" from REMD simulation
On 2010-08-21 15.05, henri mone wrote: Calculate observed "Acceptance Ratio" from REMD simulation Dear Gromacs users, I used the Gromacs how-to [1] to setup a REMD simulation. The targeted acceptance ratio was P_acp=15%, I used the temperature generator web-service [2] to get the temperature spacing. From the test simulation I want to calculate the observed acceptance ratio P_obs. The last md.log file gives a "Replica exchange statistic". I got following questions regarding on how to calculate P_obs. 1. To get P_obs from simulation I have to calculate the ratio between the successful exchange and total exchange attempts. Is this correct? I checked several papers and books (Frenkel/Smit, etc.), I only found the formula how to calculate the temperature spacing given P_acp. But I couldn't find a formula or definition how to calculate P_obs from a simulation. Is the above definition of P_obs correct? 2. The md.log file "Replica exchange statistic" gives in my case following summary [3]. For temperature T0 to T1 there wehre 664 successful exchanges. The number of exchange attempts were 1213. The ratio 664/1213 gives 55%. Would the P_obs=55% , is this correct? 3. A observed ratio of P_obs=50% given a targeted acceptance ratio of P_acp=15% is quite high. What can be the reason for this large discrepancy? Good question. We used two force fields (OPLS and GROMOS) for the development. We did however use Berendsen thermostats, which is not a good idea, and this might induce a deviation, but I would expect it to be small. The most obvious thing could be that the system used is not the one for which you input parameters on the webserver. The webserver wants the number of water molecules, if you supplied the number of atoms, that would give you a factor of three in energy. 4. Could the Gromacs users, admin etc. please add some more information to the REMD Howto [1]. In particular regarding how to calculate P_obs? It would be a really useful for the Gromacs users. Can I as a Gromacs user add some more information to the howto or do I need a login? I would appreciate any help. Thanks, Henri 1: Replica-Exchange Molecular Dynamics howto http://www.gromacs.org/Documentation/How-tos/REMD 2: Temperature generator for REMD-simulations http://folding.bmc.uu.se/remd/ 3: "md.log" file summary Replica exchange statistics Repl 2425 attempts, 1213 odd, 1212 even Repl average probabilities: Repl 0123456789 10 ... Repl .55 .55 .55 .56 .56 .54 .56 .56 .56 .56 ... Repl number of exchanges: Repl 0123456789 10 ... Repl 664 684 667 692 659 627 699 688 699 683 ... Repl average number of exchanges: Repl 0123456789 10 ... Repl .55 .56 .55 .57 .54 .52 .58 .57 .58 .56 ... -- 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] Calculate observed "Acceptance Ratio" from REMD simulation
- Original Message - From: henri mone Date: Saturday, August 21, 2010 23:06 Subject: [gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation To: gmx-users@gromacs.org > Calculate observed "Acceptance Ratio" from REMD simulation > > Dear Gromacs users, > > I used the Gromacs how-to [1] to setup a REMD simulation. The targeted > acceptance ratio was P_acp=15%, I used the temperature generator > web-service [2] to get the temperature spacing. From the test > simulation I want to calculate the observed acceptance ratio P_obs. > The last md.log file gives a "Replica exchange statistic". I got > following questions regarding on how to calculate P_obs. > > 1. To get P_obs from simulation I have to calculate the ratio between > the successful exchange and total exchange attempts. > Is this correct? I checked several papers and books (Frenkel/Smit, > etc.), I only found the formula how to calculate the temperature > spacing given P_acp. But I couldn't find a formula or definition how > to calculate P_obs from a simulation. Is the above definition of P_obs > correct? Yep. It's about the easiest thing you'll ever calculate from an MD simulation. > 2. The md.log file "Replica exchange statistic" gives in my case > following summary [3]. For temperature T0 to T1 there wehre 664 > successful exchanges. The number of exchange attempts were 1213. The > ratio 664/1213 gives 55%. Would the P_obs=55% , is this correct? > > 3. A observed ratio of P_obs=50% given a targeted acceptance > ratio of > P_acp=15% is quite high. > What can be the reason for this large discrepancy? Probably, you've not done what you've think you've done with the web server. > 4. Could the Gromacs users, admin etc. please add some more > information to the REMD Howto [1]. In particular regarding how to > calculate P_obs? It's probably not there because it's regarded as straightforward :-) > It would be a really useful for the Gromacs users. > Can I as a Gromacs user add some more information to the howto > or do I > need a login? The wiki-style web pages are largely a community effort. As such, contributions are welcome, subject to the usual wiki considerations that you might get edited mercilessly, etc. You'll need a login, and that might require someone to approve you, but that would normally be forthcoming. Mark -- 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] Error when compiled with fortran compiler in double precision
Dear gmx-users, An error was found when compiled gmx with fortran compiler in double precision, listed in the following: ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:141: error: 'nbkernel204_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:142: error: 'nbkernel210_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:143: error: 'nbkernel211_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:144: error: 'nbkernel212_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:145: error: 'nbkernel213_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:146: error: 'nbkernel214_f77_double' undeclared here (not in a function) When I check the file "nb_kernel_f77_double.c", the lines of inclusion were like this: #include "nbkernel010_f77_double.h" #include "nbkernel020_f77_double.h" #include "nbkernel030_f77_double.h" #include "nbkernel100_f77_double.h" #include "nbkernel101_f77_double.h" The naming of these header files are not consistent with the file name in dir nb_kernel_f77_double. Obviously an underline is lost here. I hope this issue will be fixed soon. Version: Gromacs-4.5b3 and the latest git vesion Command: configure --disable-float --enable-fortran ... Best Regards, Bert -- 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] How to center molecules in the box with trjconv ?
cs.org/mailing_lists/users.php >> > > -- > 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 -- Message: 8 Date: Sat, 21 Aug 2010 11:54:17 +0330 From: leila karami Subject: [gmx-users] wrong string length 0 for string buf To: gmx-users Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o com.xtc -pbc nojump -ur compact -center gromacs gives me the following error: Program trjconv, VERSION 4.0.5 Source code file: gmxfio.c, line: 609 Fatal error: wrong string length 0 for string buf (source tpxio.c, line 1641) Any suggestions would be greatly appreciated. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100821/d6c11b84/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 76, Issue 108 ** <>-- 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] editying top file after solvation
Dear gmx users, I am solvating a solute with a solvent molecule using command line below: genbox -cp solute.gro -cs solvent.gro -o solvated.gro -p solute.top solute is in a 20nm cubic box and by this command I am getting solvated box. solute.top is the top file of solute. I searched the archive list on how to edit top file for the next step which is EM of solvated molecule. I dont know how to include solvent.top file in solute.top. To do EM somehow I need to provide ff parameters of my solvent right? (also I wan to set zero charges ot all atoms so I need to do this before EM). I copied the solvent.top contents is solute top file but since atoms numbers are identical grompp em gives non atom match names error. Could you tell me what shoudl be in the [moleculetype] directory and last directory in solute.top for EM? Also I think I have to pay attention to number of solvent molecules in solvated.gro file and include it in top file I think.. - Thanks for your help, -- 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] editying top file after solvation
jojo J wrote: Dear gmx users, I am solvating a solute with a solvent molecule using command line below: genbox -cp solute.gro -cs solvent.gro -o solvated.gro -p solute.top solute is in a 20nm cubic box and by this command I am getting solvated box. solute.top is the top file of solute. I searched the archive list on how to edit top file for the next step which is EM of solvated molecule. I dont know how to include solvent.top file in solute.top. To You don't include a .top within a .top. You include an .itp within a .top, otherwise you'll get all kinds of errors related to the fact that the topology file format will be severely broken. do EM somehow I need to provide ff parameters of my solvent right? (also I wan to set zero charges ot all atoms so I need to do this before EM). You should only set all charges to zero if that's an appropriate model. I can hardly think of a case where that would be appropriate... I copied the solvent.top contents is solute top file but since atoms numbers are identical grompp em gives non atom match names error. Could you tell me what shoudl be in the [moleculetype] directory and last directory in solute.top for EM? Also I think I have to pay attention to number of solvent molecules in solvated.gro file and include it in top file I think.. You need to spend some time with the manual, Chapter 5. Your solute and solvent should be separate [moleculetype] directives, for which all atom number is sequential and starts from zero. Do any of the basic tutorials and look at how this is done for a simple protein in water. Of particular educational value would be the grompp-processed topology (grompp -pp), which will show you the entire contents of the topology, expanded based on everything that was #included. http://www.gromacs.org/Documentation/Tutorials#General -Justin - Thanks for your help, -- 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
