[gmx-users] How to calculate the dihedral angle variations ???
Hi Everyone ! How can i see the variations in the Cβ-S-S-Cβ (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? Mensaje citado por Justin A. Lemkul jalem...@vt.edu: Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observables. Empirical fitting of the initial parameters may be required. Refer to the primary literature. The reference for the 53a5 and 53a6 parameter sets are published in JCC, which may provide you with some useful information. -Justin -- From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Sent: Friday, March 27, 2009 2:35 PM To: bije...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassignedones Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that I find would help me to make my ideas more clear: 1-am I overestimating the importance of ligand charges in such a simple study of protein-small molecule (containg charged Phosphate groups) complex? or 1.1-The only way to test for this is doing many different simulation on the same system using different type of computed charges to see what happen? 2-How could I try to choose a method to obtain reasonable charges based on the
Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Lucio Ricardo Montero Valenzuela wrote: So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? We don't support United atom OPLS because Jorgensen himself does not use it anymore. That if something should indicate for you that the united atom force field has been superseded by the all-atom. Jorgensen himself uses OPLS-AA with TIP4P, so this is probably the best recommendation. Most important, if you chose to use another combination, you basically have to prove that this works as well (whatever that means...) Mensaje citado por Justin A. Lemkul jalem...@vt.edu: Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observables. Empirical fitting of the initial parameters may be required. Refer to the primary literature. The reference for the 53a5 and 53a6 parameter sets are published in JCC, which may provide you with some useful information. -Justin -- From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Sent: Friday, March 27, 2009 2:35 PM To: bije...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassignedones Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that I find would help me to make my ideas more clear: 1-am I overestimating the importance of ligand charges in such a simple study
Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Hi, I've recently used OPLS-AA for a similar calculation. It has the advantage that many atom types are already defined in Gromacs and that QM-based calculations give you reasonable charges. Note that it may take considerable simulation time (tens of ns) to discriminate between similar docked poses of the same molecule, though MD can give you a hint. If things were easier docking programs would do a better job. Ran. On Wed, 01 Apr 2009 00:12:31 -0600 Lucio Ricardo Montero Valenzuela lucio...@ibt.unam.mx wrote: So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? Mensaje citado por Justin A. Lemkul jalem...@vt.edu: Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observables. Empirical fitting of the initial parameters may be required. Refer to the primary literature. The reference for the 53a5 and 53a6 parameter sets are published in JCC, which may provide you with some useful information. -Justin -- From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Sent: Friday, March 27, 2009 2:35 PM To: bije...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassignedones Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that
RE: [gmx-users] Energy Conservation with 4fs timestep
Date: Wed, 1 Apr 2009 14:15:05 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Energy Conservation with 4fs timestep Joe Joe wrote: Hi, I get good conservation when running NVE in gromacs with 4 fs when I use PME-switch for electrostatics but not so good when I use switch. Any thoughts why that would be? Params shown below. Finite cutoffs (such as used with switch) are intrinsically unlikely to conserve energy. Mark That is not right. Finite cut-off's such as switch and shift are purposely designed to conserve energy. Switch is not particularly good though, since the switching introduces large forces. I would advise to use PME-switch or reaction-field-zero for electrostatics and shift for vdw. But the main problem in your setup seems to be the 0.1 nm buffer between the cut-off and rlist. In general you will need a buffer of 0.25 to 0.3 nm. You can use rlist=-1 to get exact integration and then vary rlist to get a reasonable neighborlist update frequency (somewhere around 10 steps). We should automate the choice of rlist such that the user does not need to worry about this. Berk _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.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] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
I wanted the OPLS-UA because my system is large (3 proteins with 2 organic molecules, in water), and, if the G43a1 forcefield gives me a MD speed of 70 ps/day, an all atom model will result much slower. So what else can I do to speed up my MD, to get results in 1-3 months?. Mensaje citado por David van der Spoel sp...@xray.bmc.uu.se: Lucio Ricardo Montero Valenzuela wrote: So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? We don't support United atom OPLS because Jorgensen himself does not use it anymore. That if something should indicate for you that the united atom force field has been superseded by the all-atom. Jorgensen himself uses OPLS-AA with TIP4P, so this is probably the best recommendation. Most important, if you chose to use another combination, you basically have to prove that this works as well (whatever that means...) Mensaje citado por Justin A. Lemkul jalem...@vt.edu: Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observables. Empirical fitting of the initial parameters may be required. Refer to the primary literature. The reference for the 53a5 and 53a6 parameter sets are published in JCC, which may provide you with some useful information. -Justin -- From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Sent: Friday, March 27, 2009 2:35 PM To: bije...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassignedones Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand
RE: [gmx-users] How to calculate the dihedral angle variations ???
Did you try g_angle?? Antonia Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the Cβ-S-S-Cβ (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD _ More than messages-check out the rest of the Windows LiveT. http://www.microsoft.com/windows/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 calculate the dihedral angle variations ???
First of all Thanks for ur reply ! I tried both g_angle and g_chi with all suitable options, but i didn't get the required result.Can u plz help me in this regard ??? 2009/4/1 Antonia V. antonia_h...@hotmail.com Did you try g_angle?? Antonia -- Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the Cβ-S-S-Cβ (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD -- check out the rest of the Windows LiveT. More than mail-Windows LiveT goes way beyond your inbox. More than messageshttp://www.microsoft.com/windows/windowslive/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 subject)
Hello, I am trying to simulate a system at the NVT ensemble, but after a few steps I get the error [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault Any ideas what this means?? Thank you Antonia _ Drag n’ drop—Get easy photo sharing with Windows Live™ Photos. http://www.microsoft.com/windows/windowslive/products/photos.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.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 calculate the dihedral angle variations ???
Hi Venkat, What exactly do you mean with variations. Do you want to follow the angle over time, or do you want distributions with mean and variance estimates? g_angle and g_chi seem to be the appropriate tools. You mention you tried all suitable options, but fail to explain what you tried and what exactly it is you want. We need that sort of information to be able to help you out. Cheers, Tsjerk 2009/4/1 Venkat Reddy venkat...@gmail.com: First of all Thanks for ur reply ! I tried both g_angle and g_chi with all suitable options, but i didn't get the required result.Can u plz help me in this regard ??? 2009/4/1 Antonia V. antonia_h...@hotmail.com Did you try g_angle?? Antonia Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the Cβ-S-S-Cβ (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD check out the rest of the Windows LiveT. More than mail-Windows LiveT goes way beyond your inbox. More than messages ___ gmx-users mailing list gmx-us...@gromacs.org http://www.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 -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing list gmx-us...@gromacs.org http://www.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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 calculate the dihedral angle variations ???
Hai Sir ! Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over time.I used the commands g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type dihedral -all g_chi -s gp123_full.gro -f gp123_full.trr -o order.xvg -jc Jcoupling.xvg -g chi.log -rama -all Please suggest me the right options Thanks for ur concern 2009/4/1 Tsjerk Wassenaar tsje...@gmail.com Hi Venkat, What exactly do you mean with variations. Do you want to follow the angle over time, or do you want distributions with mean and variance estimates? g_angle and g_chi seem to be the appropriate tools. You mention you tried all suitable options, but fail to explain what you tried and what exactly it is you want. We need that sort of information to be able to help you out. Cheers, Tsjerk 2009/4/1 Venkat Reddy venkat...@gmail.com: First of all Thanks for ur reply ! I tried both g_angle and g_chi with all suitable options, but i didn't get the required result.Can u plz help me in this regard ??? 2009/4/1 Antonia V. antonia_h...@hotmail.com Did you try g_angle?? Antonia Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the Cβ-S-S-Cβ (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD check out the rest of the Windows LiveT. More than mail-Windows LiveT goes way beyond your inbox. More than messages ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Gromacs 4.0.2 vs. 4.0.3
Hi, we performed for comparison pentadecane simulations using both the 4.0.2 version and 4.0.3, with the same mdp file (see below). Results look quite different (reproducible), for 4.0.2 the system quickly (few 100 ps) enters the crystalline phase while it stays fluid for 4.0.3 (with an increased volume/molecule). Is this due to some known bug in 4.0.2? Best Rainer integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= System ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 1 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc_grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 280 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1. compressibility = 8.82e-5 ref_p= 1. ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen_temp = 280 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = h-bonds ; Type of constraint algorithm constraint_algorithm = Lincs ; Do not constrain the start configuration continuation = no Shake-SOR= no shake_tol= 1e-04 lincs_order = 4 lincs-iter = 1 incs_warnangle = 30 morse= no __ Dr. Rainer Böckmann Theoretical Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: rai...@bioinformatik.uni-saarland.de http://www.bioinf.uni-sb.de/RB/ ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Error with equilibration of DPPC membrane with protein
Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), and position restraints on the protein, I have also merged Cl and SOL in the same temp group, but it does not seem to work anyway. We still get the LINCS warnings. Thankful for all help! /Edvin Edvin Erdtman wrote: Hi again an Thank you for comments! Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used position restraints for the protein as mentioned in Methods 41 (2007) 475-488. We have tried with a scaling factor of 0,95 and 0,97, and a cut-off value of 14 to expand the box and 0 to reduce the box (is that ok???). perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5 em2/area.dat with scaling factor 0.95 23 steps were needed, and with 0,97 39 steps were followed. This seems reasonable. When we have not used position restraints for the protein, and used a cutoff value of 4 Å, the simulation were performed well even without annealing. 4 A cutoff? For what? That is far too short for a lipid bilayer simulation. Or am I misunderstanding where you are applying this 4 A? Is it part of InflateGRO? Yes that is a cut-off for the InflateGRO. cutoff of distance between alpha-carbon of protein and phosphorus atoms in DPPC (0 in the upper example of running the perl script). If the distance are within this value, then that DPPC will be removed. I thought that this parameter was used only in the diverging step with Inflategro, not when compressing the system. Therefore we tried to run calculations with that parameter set to 0 instead (above). We have tried to energy minimize the system with steepest descent method in each step of decreasing the box. Do each of these minimizations complete satisfactorily? Most of them converged to Fmax 1000. After water soaking, we have tried with both cg and steep energy minimizations. The problems we are facing: - All the energy minimizations are not reaching Fmax 1000 How close to Fmax are you getting? If it's still on the order of 10^3 you may be OK; if it's a lot larger then you have other problems to deal with. The highest force we got (using scaling factor = 0.97) at step 33: Maximum force = 2.6218958e+03 on atom 4591 snip tcoupl = Nose-hoover tc-grps = DPPC Cl SOL Protein tau_t= 0.1 0.1 0.1 0.1 ref_t= 100 100 100 100 Here is a potential problem. Never couple solvent and ions separately. Make an index group of these two merged species. See here: http://wiki.gromacs.org/index.php/thermostats Thank you for that advice, I will do that. But really I don't think that is our main problem. We tried also without chlorine (system total charge of +2), but we got the same error. Another bit of general advice. I had a very mysterious problem once where during equilibration of a DPPC bilayer my lipids were blowing apart for no apparent reason. Upon very close inspection of the trajectory (setting nstxout = 1) I identified the initial location of the explosion. A Cl- ion was immediately next to a phosphate oxygen (very hard to see!), and it was causing a huge force that was ripping my lipid apart. Just an idea, if the InflateGRO minimizations are working OK, but the solvated system with ions is not working. -Justin Thankful for all help we can get! /Edvin and Sujith /Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 begin:vcard fn:Edvin Erdtman n:Erdtman;Edvin org;quoted-printable:=C3=96rebro University;Biophysical Chemistry, School of Science and Technology adr;quoted-printable:;;;=C3=96rebro;;701 82 ;Sweden email;internet:edvin.erdt...@oru.se title:Fil. Lic. tel;work:019-30 13 81 tel;fax:019-30 35 66 x-mozilla-html:TRUE url:http://www.oru.se/nat/Edvin_Erdtman version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post
Re: [gmx-users] Error with equilibration of DPPC membrane with protein
Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), and position restraints on the protein, I have also merged Cl and SOL in the same temp group, but it does not seem to work anyway. We still get the LINCS warnings. Why are you using a cutoff during the compression phase? You will continue to delete lipids! I have never had a problem if I scale up by a factor of 4, with a 1.4-nm cutoff, then compress by a factor of 0.95 (with no cutoff). Maybe that will make a difference? -Justin Thankful for all help! /Edvin Edvin Erdtman wrote: Hi again an Thank you for comments! Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used position restraints for the protein as mentioned in Methods 41 (2007) 475-488. We have tried with a scaling factor of 0,95 and 0,97, and a cut-off value of 14 to expand the box and 0 to reduce the box (is that ok???). perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5 em2/area.dat with scaling factor 0.95 23 steps were needed, and with 0,97 39 steps were followed. This seems reasonable. When we have not used position restraints for the protein, and used a cutoff value of 4 Å, the simulation were performed well even without annealing. 4 A cutoff? For what? That is far too short for a lipid bilayer simulation. Or am I misunderstanding where you are applying this 4 A? Is it part of InflateGRO? Yes that is a cut-off for the InflateGRO. cutoff of distance between alpha-carbon of protein and phosphorus atoms in DPPC (0 in the upper example of running the perl script). If the distance are within this value, then that DPPC will be removed. I thought that this parameter was used only in the diverging step with Inflategro, not when compressing the system. Therefore we tried to run calculations with that parameter set to 0 instead (above). We have tried to energy minimize the system with steepest descent method in each step of decreasing the box. Do each of these minimizations complete satisfactorily? Most of them converged to Fmax 1000. After water soaking, we have tried with both cg and steep energy minimizations. The problems we are facing: - All the energy minimizations are not reaching Fmax 1000 How close to Fmax are you getting? If it's still on the order of 10^3 you may be OK; if it's a lot larger then you have other problems to deal with. The highest force we got (using scaling factor = 0.97) at step 33: Maximum force = 2.6218958e+03 on atom 4591 snip tcoupl = Nose-hoover tc-grps = DPPC Cl SOL Protein tau_t= 0.1 0.1 0.1 0.1 ref_t= 100 100 100 100 Here is a potential problem. Never couple solvent and ions separately. Make an index group of these two merged species. See here: http://wiki.gromacs.org/index.php/thermostats Thank you for that advice, I will do that. But really I don't think that is our main problem. We tried also without chlorine (system total charge of +2), but we got the same error. Another bit of general advice. I had a very mysterious problem once where during equilibration of a DPPC bilayer my lipids were blowing apart for no apparent reason. Upon very close inspection of the trajectory (setting nstxout = 1) I identified the initial location of the explosion. A Cl- ion was immediately next to a phosphate oxygen (very hard to see!), and it was causing a huge force that was ripping my lipid apart. Just an idea, if the InflateGRO minimizations are working OK, but the solvated system with ions is not working. -Justin Thankful for all help we can get! /Edvin and Sujith /Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
RE: [gmx-users] Gromacs 4.0.2 vs. 4.0.3
Hi, The release notes for 4.0.3 are at: http://www.gromacs.org/content/view/181/132/ I don't see any relevant bug fixes there and I don't recall any either. Please update to 4.0.4, since many small bugs have been fixed. Berk From: rai...@bioinformatik.uni-saarland.de To: gmx-users@gromacs.org Date: Wed, 1 Apr 2009 11:20:53 +0200 CC: Subject: [gmx-users] Gromacs 4.0.2 vs. 4.0.3 Hi, we performed for comparison pentadecane simulations using both the 4.0.2 version and 4.0.3, with the same mdp file (see below). Results look quite different (reproducible), for 4.0.2 the system quickly (few 100 ps) enters the crystalline phase while it stays fluid for 4.0.3 (with an increased volume/molecule). Is this due to some known bug in 4.0.2? Best Rainer integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= System ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 1 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc_grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 280 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1. compressibility = 8.82e-5 ref_p= 1. ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen_temp = 280 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = h-bonds ; Type of constraint algorithm constraint_algorithm = Lincs ; Do not constrain the start configuration continuation = no Shake-SOR= no shake_tol= 1e-04 lincs_order = 4 lincs-iter = 1 incs_warnangle = 30 morse= no __ Dr. Rainer Böckmann Theoretical Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: rai...@bioinformatik.uni-saarland.de http://www.bioinf.uni-sb.de/RB/ ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] GROMOS carbohydrate forcefield 45a4
Dear List, In the paper entitled A new GROMOS force field for hexopyranose-based carbohydrates Journal of Computational Chemistry Volume 26 Issue 13, Pages 1400 - 1412. When the authors ran unrestrained md for 2ns, once the conformation is stabilised in chair, they donot observe any further transitions. Another paper describes the inversions of the pyranose ring within a 1-ns MD simulation at 600 K. I m running NPT simulations at 310 as well as 400 K of sulfated pyranose rings using GROMOS ff in gromacs. I start my simulation with boat conformation which intercoverts to chair within 60 ps but I cannot see the transitions back and forth. Of,course I see transitions back and forth when i increase the temperature to 800K. Did any body try to simulate such sugars where they observe boat-chair-boat transitions using GROMOS? How long did it took? Was it at room temperature? What parameters are important to validate ff for such molecules? Your help is appreciated. -- Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Error with equilibration of DPPC membrane with protein
Hi We have tried with no cutoff, as I have written in former emails, but that was when we got trouble with LINCS warnings. We then thought that we could try to continue remove lipids in the compression-steps to get rid of that LINCS warnings, and to have a stable system! Is it maybe the protein that is the problem - need to be more minimized? /Edvin Justin A. Lemkul wrote: Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), and position restraints on the protein, I have also merged Cl and SOL in the same temp group, but it does not seem to work anyway. We still get the LINCS warnings. Why are you using a cutoff during the compression phase? You will continue to delete lipids! I have never had a problem if I scale up by a factor of 4, with a 1.4-nm cutoff, then compress by a factor of 0.95 (with no cutoff). Maybe that will make a difference? -Justin begin:vcard fn:Edvin Erdtman n:Erdtman;Edvin org;quoted-printable:=C3=96rebro University;Biophysical Chemistry, School of Science and Technology adr;quoted-printable:;;;=C3=96rebro;;701 82 ;Sweden email;internet:edvin.erdt...@oru.se title:Fil. Lic. tel;work:019-30 13 81 tel;fax:019-30 35 66 x-mozilla-html:TRUE url:http://www.oru.se/nat/Edvin_Erdtman version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Error with equilibration of DPPC membrane with protein
Edvin Erdtman wrote: Hi We have tried with no cutoff, as I have written in former emails, but that was when we got trouble with LINCS warnings. We then thought that we could try to continue remove lipids in the compression-steps to get rid of that LINCS warnings, and to have a stable system! Is it maybe the protein that is the problem - need to be more minimized? Maybe yes, maybe no. If I remember your original post, you are doing the annealing with Nose-Hoover as the thermostat. IIRC, N-H does not respond well to changes in temperature (it fluctuates a lot). Maybe try your protocol using a weak coupling scheme, Berendsen or V-rescale? -Justin /Edvin Justin A. Lemkul wrote: Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), and position restraints on the protein, I have also merged Cl and SOL in the same temp group, but it does not seem to work anyway. We still get the LINCS warnings. Why are you using a cutoff during the compression phase? You will continue to delete lipids! I have never had a problem if I scale up by a factor of 4, with a 1.4-nm cutoff, then compress by a factor of 0.95 (with no cutoff). Maybe that will make a difference? -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.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 with equilibration of DPPC membrane with protein
Try gromacs 3.1.4 make_hole version, downloadable from the user contributions page. This works well for me. Alternatively, just select a bunch of lipids to remove based on g_mindist and equilibrate -- 50ns is cheap nowadays. The only reason that inflategro might be a huge advantage is if you plan to simulate a large number of different systems and you want to automate the procedure. Chris. -- original message -- Edvin Erdtman wrote: Hi We have tried with no cutoff, as I have written in former emails, but that was when we got trouble with LINCS warnings. We then thought that we could try to continue remove lipids in the compression-steps to get rid of that LINCS warnings, and to have a stable system! Is it maybe the protein that is the problem - need to be more minimized? Maybe yes, maybe no. If I remember your original post, you are doing the annealing with Nose-Hoover as the thermostat. IIRC, N-H does not respond well to changes in temperature (it fluctuates a lot). Maybe try your protocol using a weak coupling scheme, Berendsen or V-rescale? -Justin /Edvin Justin A. Lemkul wrote: Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), and position restraints on the protein, I have also merged Cl and SOL in the same temp group, but it does not seem to work anyway. We still get the LINCS warnings. Why are you using a cutoff during the compression phase? You will continue to delete lipids! I have never had a problem if I scale up by a factor of 4, with a 1.4-nm cutoff, then compress by a factor of 0.95 (with no cutoff). Maybe that will make a difference? -Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 subject)
1. A description of your system I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750 atoms. 2. Anything else that was printed to screen or the .log file (that's where the real error message will appear) On the screen the message was [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault and the last thing that was written in the md.log file is Step Time Lambda 00.00.0 Grid: 8 x 8 x 8 cells Energies (kJ/mol) Bond AngleProper Dih.LJ (SR) Coulomb (SR) 3.12078e+037.44768e+045.19128e+03 -1.67708e+04 -1.07965e+03 Coul. recip. PotentialKinetic En. Total EnergyTemperature -6.75318e+035.81852e+042.02196e+015.82054e+043.41383e-01 Pressure (bar) -2.55714e+03 3. What happened in the EM procedure? After the EM (steep) the forces were minimized to the desired accuracy (Tolerance (Fmax) = 1.0e+02) 4. What .mdp parameters you are using I use a time step of 2fs, PME for the electrostatics, a quite large cut-off (1.2), the nose-hoover thermostat (340K) 5. Which Gromacs version you are using I use GROMACS 4.0.3 Thank you Antonia Date: Wed, 1 Apr 2009 06:39:17 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] (no subject) Antonia V. wrote: Hello, I am trying to simulate a system at the NVT ensemble, but after a few steps I get the error [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault Any ideas what this means?? Given this information, no. Segmentation faults are difficult to pin down, anyway, but if you want help, you'll have to provide more useful information: 1. A description of your system 2. Anything else that was printed to screen or the .log file (that's where the real error message will appear) 3. What happened in the EM procedure? 4. What .mdp parameters you are using 5. Which Gromacs version you are using -Justin Thank you Antonia What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.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 _ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 subject)
Antonia V. wrote: 1. A description of your system I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750 atoms. 2. Anything else that was printed to screen or the .log file (that's where the real error message will appear) On the screen the message was [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault and the last thing that was written in the md.log file is Step Time Lambda 00.00.0 Grid: 8 x 8 x 8 cells Energies (kJ/mol) Bond AngleProper Dih.LJ (SR) Coulomb (SR) 3.12078e+037.44768e+045.19128e+03 -1.67708e+04 -1.07965e+03 Coul. recip. PotentialKinetic En. Total EnergyTemperature -6.75318e+035.81852e+042.02196e+015.82054e+043.41383e-01 Pressure (bar) -2.55714e+03 Your potential energy has spiked to a very large value. That indicates you still have some bad contacts in the system. 3. What happened in the EM procedure? After the EM (steep) the forces were minimized to the desired accuracy (Tolerance (Fmax) = 1.0e+02) Was the potential reasonable? See above. 4. What .mdp parameters you are using I use a time step of 2fs, PME for the electrostatics, a quite large cut-off (1.2), the nose-hoover thermostat (340K) Well, these are not all of your parameters, surely (it's best to post your whole .mdp file). If you are going for 340 K, you can see from your .log file that the temperature is actually 0.34 K. Are you doing some sort of annealing protocol? Again, it's best to give complete information :) Nose-Hoover is a poor choice for initial equilibration, if this is what you are doing. It allows greater temperature fluctuation. Start with Berendsen or V-rescale for some time, then switch to N-H when collecting your real data, if N-H is your choice for thermostat. Is a .trr ever output? If it is, you can view the trajectory to see where things are going wrong. If you don't get a .trr, then set nstxout = 1 in the .mdp file to hopefully get a frame or two of where the problem may lie. -Justin 5. Which Gromacs version you are using I use GROMACS 4.0.3 Thank you Antonia Date: Wed, 1 Apr 2009 06:39:17 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] (no subject) Antonia V. wrote: Hello, I am trying to simulate a system at the NVT ensemble, but after a few steps I get the error [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault Any ideas what this means?? Given this information, no. Segmentation faults are difficult to pin down, anyway, but if you want help, you'll have to provide more useful information: 1. A description of your system 2. Anything else that was printed to screen or the .log file (that's where the real error message will appear) 3. What happened in the EM procedure? 4. What .mdp parameters you are using 5. Which Gromacs version you are using -Justin Thank you Antonia What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
RE: [gmx-users] (no subject)
I switched to v-rescale for the thermostat and things look normal! Thanks for the help Antonia Date: Wed, 1 Apr 2009 12:11:47 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] (no subject) Antonia V. wrote: 1. A description of your system I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750 atoms. 2. Anything else that was printed to screen or the .log file (that's where the real error message will appear) On the screen the message was [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault and the last thing that was written in the md.log file is Step Time Lambda 00.00.0 Grid: 8 x 8 x 8 cells Energies (kJ/mol) Bond AngleProper Dih.LJ (SR) Coulomb (SR) 3.12078e+037.44768e+045.19128e+03 -1.67708e+04 -1.07965e+03 Coul. recip. PotentialKinetic En. Total EnergyTemperature -6.75318e+035.81852e+042.02196e+015.82054e+043.41383e-01 Pressure (bar) -2.55714e+03 Your potential energy has spiked to a very large value. That indicates you still have some bad contacts in the system. 3. What happened in the EM procedure? After the EM (steep) the forces were minimized to the desired accuracy (Tolerance (Fmax) = 1.0e+02) Was the potential reasonable? See above. 4. What .mdp parameters you are using I use a time step of 2fs, PME for the electrostatics, a quite large cut-off (1.2), the nose-hoover thermostat (340K) Well, these are not all of your parameters, surely (it's best to post your whole .mdp file). If you are going for 340 K, you can see from your .log file that the temperature is actually 0.34 K. Are you doing some sort of annealing protocol? Again, it's best to give complete information :) Nose-Hoover is a poor choice for initial equilibration, if this is what you are doing. It allows greater temperature fluctuation. Start with Berendsen or V-rescale for some time, then switch to N-H when collecting your real data, if N-H is your choice for thermostat. Is a .trr ever output? If it is, you can view the trajectory to see where things are going wrong. If you don't get a .trr, then set nstxout = 1 in the .mdp file to hopefully get a frame or two of where the problem may lie. -Justin 5. Which Gromacs version you are using I use GROMACS 4.0.3 Thank you Antonia Date: Wed, 1 Apr 2009 06:39:17 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] (no subject) Antonia V. wrote: Hello, I am trying to simulate a system at the NVT ensemble, but after a few steps I get the error [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault Any ideas what this means?? Given this information, no. Segmentation faults are difficult to pin down, anyway, but if you want help, you'll have to provide more useful information: 1. A description of your system 2. Anything else that was printed to screen or the .log file (that's where the real error message will appear) 3. What happened in the EM procedure? 4. What .mdp parameters you are using 5. Which Gromacs version you are using -Justin Thank you Antonia What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx ___ gmx-users mailing list gmx-users@gromacs.org http://www.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] Problems with Jacobi diagonalization
Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ gmx-users mailing list gmx-us...@gromacs.org http://www.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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Energy Conservation with 4fs timestep
rlist 1.3 did the trick, thanks. Why did I not see this problem with PME-switch? Thanks, Ilya 2009/4/1 Berk Hess g...@hotmail.com Date: Wed, 1 Apr 2009 14:15:05 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Energy Conservation with 4fs timestep Joe Joe wrote: Hi, I get good conservation when running NVE in gromacs with 4 fs when I use PME-switch for electrostatics but not so good when I use switch. Any thoughts why that would be? Params shown below. Finite cutoffs (such as used with switch) are intrinsically unlikely to conserve energy. Mark That is not right. Finite cut-off's such as switch and shift are purposely designed to conserve energy. Switch is not particularly good though, since the switching introduces large forces. I would advise to use PME-switch or reaction-field-zero for electrostatics and shift for vdw. But the main problem in your setup seems to be the 0.1 nm buffer between the cut-off and rlist. In general you will need a buffer of 0.25 to 0.3 nm. You can use rlist=-1 to get exact integration and then vary rlist to get a reasonable neighborlist update frequency (somewhere around 10 steps). We should automate the choice of rlist such that the user does not need to worry about this. Berk -- Express yourself instantly with MSN Messenger! MSN Messengerhttp://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] x2top Encad all-atom force field (vacuum) not recognizing bonds
Dear All, I have been trying to determine why I am experiencing problems when I run a gromacs file through x2top. I have checked my gromacs file with VMD to ensure that the file is correct and VMD validates that my file is correct as I see the intended structure. Thus, the atoms are indeed located within reasonable distance from each other such that x2top should be recognizing the bonds. Here is an extract from my gromacs file: 2Grph C1 0.000 0.000 0.000 0. 0. 0. 2Grph C2 0.071 -0.123 0.000 0. 0. 0. 2Grph C3 0.071 0.123 0.000 0. 0. 0. 2Grph C4 -0.142 0.000 0.000 0. 0. 0. 2Grph C5 -0.000 -0.250 0.000 0. 0. 0. 2Grph C6 0.210 -0.120 0.000 0. 0. 0. I thought that in order to make x2top work correctly that I would have to modify the files as described in Christopher Stiles website (http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the following files and saved them in my working directory: ffencadv.n2t ffgmx.n2t ffgmxbon.itp I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in one post that this file should be renamed as such. After all these changes, I still experience a problem when I run the command: x2top -ff select -f graphene_nm.gro -o graphene_nm.top selecting option 7: Encad all-atom force field, using scaled-down vacuum charges When I run the above command, I receive output telling me that the atoms have 0 bonds. An extract of the output appears below for your reference. Can not find forcefield for atom H-266 with 0 bonds Can not find forcefield for atom H-267 with 0 bonds Can not find forcefield for atom H-268 with 0 bonds Can not find forcefield for atom H-269 with 0 bonds Can not find forcefield for atom H-270 with 0 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 270 atoms --- Could you please help me resolve this issue? Thank you in advance for your assistance. Darrell Koskinen ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] x2top Encad all-atom force field (vacuum) not recognizing bonds
darre...@ece.ubc.ca wrote: Dear All, I have been trying to determine why I am experiencing problems when I run a gromacs file through x2top. I have checked my gromacs file with VMD to ensure that the file is correct and VMD validates that my file is correct as I see the intended structure. Thus, the atoms are indeed located within reasonable distance from each other such that x2top should be recognizing the bonds. Here is an extract from my gromacs file: 2Grph C1 0.000 0.000 0.000 0. 0. 0. 2Grph C2 0.071 -0.123 0.000 0. 0. 0. 2Grph C3 0.071 0.123 0.000 0. 0. 0. 2Grph C4 -0.142 0.000 0.000 0. 0. 0. 2Grph C5 -0.000 -0.250 0.000 0. 0. 0. 2Grph C6 0.210 -0.120 0.000 0. 0. 0. I thought that in order to make x2top work correctly that I would have to modify the files as described in Christopher Stiles website (http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the following files and saved them in my working directory: ffencadv.n2t ffgmx.n2t ffgmxbon.itp I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in one post that this file should be renamed as such. After all these changes, I still experience a problem when I run the command: x2top -ff select -f graphene_nm.gro -o graphene_nm.top selecting option 7: Encad all-atom force field, using scaled-down vacuum charges When I run the above command, I receive output telling me that the atoms have 0 bonds. An extract of the output appears below for your reference. Can not find forcefield for atom H-266 with 0 bonds Can not find forcefield for atom H-267 with 0 bonds Can not find forcefield for atom H-268 with 0 bonds Can not find forcefield for atom H-269 with 0 bonds Can not find forcefield for atom H-270 with 0 bonds Could there still be an error in your gro file, as it seems to contain only C, and the error message points to H. x2top might work slightly better in 4.0.x. And by the way, this tutorial may be slightly confusing. The only thing you need to do is edit the .n2t file corresponding to your force field. I don't recall what is supplied in 3.3, but in 4.0 it is ffoplsaa.n2t. --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 270 atoms --- Could you please help me resolve this issue? Thank you in advance for your assistance. Darrell Koskinen ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David. David van der Spoel, PhD, Professor of Biology 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 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problems with Jacobi diagonalization
Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] Problems with Jacobi diagonalization
Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 mailto: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://www.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 -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
RE: [gmx-users] How to calculate the dihedral angle variations ???
g_angle will do that fine, and with the options you used it should have done so. Possible issue that may make that fail is you failed to generate the correct angle index file for the dihedral(s) of interest. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Venkat Reddy Sent: Wednesday, 1 April 2009 7:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to calculate the dihedral angle variations ??? Hai Sir ! Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over time.I used the commands g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type dihedral -all g_chi -s gp123_full.gro -f gp123_full.trr -o order.xvg -jc Jcoupling.xvg -g chi.log -rama -all Please suggest me the right options Thanks for ur concern 2009/4/1 Tsjerk Wassenaar tsje...@gmail.com Hi Venkat, What exactly do you mean with variations. Do you want to follow the angle over time, or do you want distributions with mean and variance estimates? g_angle and g_chi seem to be the appropriate tools. You mention you tried all suitable options, but fail to explain what you tried and what exactly it is you want. We need that sort of information to be able to help you out. Cheers, Tsjerk 2009/4/1 Venkat Reddy venkat...@gmail.com: First of all Thanks for ur reply ! I tried both g_angle and g_chi with all suitable options, but i didn't get the required result.Can u plz help me in this regard ??? 2009/4/1 Antonia V. antonia_h...@hotmail.com Did you try g_angle?? Antonia Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the Cβ-S-S-Cβ (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD check out the rest of the Windows LiveT. More than mail-Windows LiveT goes way beyond your inbox. More than messages ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR,
Re: [gmx-users] Problems with Jacobi diagonalization
Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. ~Dayle On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problems with Jacobi diagonalization
Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. -Justin ~Dayle On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post
Re: [gmx-users] Problems with Jacobi diagonalization
Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. Or use tpbconv - this is the other application for that utility. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problems with Jacobi diagonalization
Or rather than modifying the .top use tpbconv with an index file to generate a new .tpr Tom --On Wednesday, April 01, 2009 21:15:34 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. -Justin ~Dayle On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Problems with Jacobi diagonalization
Thanks, Mark- I re-ran a short MD simulation with TDR as the only xtc group, and used tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar with an index.ndx that contains only TPR (just to be safe!), g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx and I still get the Jacobi error: Choose a group for the least squares fit Group 0 ( TDR) has29 elements There is one group in the index Choose a group for the covariance analysis Group 0 ( TDR) has29 elements There is one group in the index Calculating the average structure ... Reading frame 0 time0.000 --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI ~Dayle On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. Or use tpbconv - this is the other application for that utility. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] x2top Encad all-atom force field (vacuum)
Date: Wed, 01 Apr 2009 22:38:28 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] x2top Encad all-atom force field (vacuum) not recognizing bonds To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49d3d0c4.4040...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Dear All, I have been trying to determine why I am experiencing problems when I run a gromacs file through x2top. I have checked my gromacs file with VMD to ensure that the file is correct and VMD validates that my file is correct as I see the intended structure. Thus, the atoms are indeed located within reasonable distance from each other such that x2top should be recognizing the bonds. Here is an extract from my gromacs file: 2Grph C1 0.000 0.000 0.000 0. 0. 0. 2Grph C2 0.071 -0.123 0.000 0. 0. 0. 2Grph C3 0.071 0.123 0.000 0. 0. 0. 2Grph C4 -0.142 0.000 0.000 0. 0. 0. 2Grph C5 -0.000 -0.250 0.000 0. 0. 0. 2Grph C6 0.210 -0.120 0.000 0. 0. 0. I thought that in order to make x2top work correctly that I would have to modify the files as described in Christopher Stiles website (http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the following files and saved them in my working directory: ffencadv.n2t ffgmx.n2t ffgmxbon.itp I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in one post that this file should be renamed as such. After all these changes, I still experience a problem when I run the command: x2top -ff select -f graphene_nm.gro -o graphene_nm.top selecting option 7: Encad all-atom force field, using scaled-down vacuum charges When I run the above command, I receive output telling me that the atoms have 0 bonds. An extract of the output appears below for your reference. Can not find forcefield for atom H-266 with 0 bonds Can not find forcefield for atom H-267 with 0 bonds Can not find forcefield for atom H-268 with 0 bonds Can not find forcefield for atom H-269 with 0 bonds Can not find forcefield for atom H-270 with 0 bonds Could there still be an error in your gro file, as it seems to contain only C, and the error message points to H. x2top might work slightly better in 4.0.x. And by the way, this tutorial may be slightly confusing. The only thing you need to do is edit the .n2t file corresponding to your force field. I don't recall what is supplied in 3.3, but in 4.0 it is ffoplsaa.n2t. My gro file does contain H atoms as well. In my extract of the gro file I only showed the first few lines of the gro file and these lines only have C atoms. Note that I receive the same message for the C atoms (i.e. Can not find forcefield for atom C-1 with 0 bonds). I actually created the files ffencadv.n2t ffgmx.n2t in my working directory since the only n2t file I could find in the gromacs directory was the ffoplsaa.n2t file and the tutorial did not mention the ffoplsaa.n2t file. Should I be modifying the ffoplsaa.n2t file instead? If so, can you please provide me some direction on what needs to be added to this file so that it recognizes the atoms in my graphene structure as I looked at this file but do not understand what some of the columns represent. Also, I thought that ffoplsaa was to be used for liquids and since my simulation is in an air environment, I thought that I should be using the encad force field in a vacuum and should therefore be modifying an encad n2t file. Please correct me if I am wrong. Also, could you also please explain the purpose of the n2t file as I looked in the gromacs manual and see no description of files with the n2t extension and their purpose. Thanks again in advance. Darrell --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 270 atoms --- Could you please help me resolve this issue? Thank you in advance for your assistance. Darrell Koskinen ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David. David van der Spoel, PhD, Professor of Biology 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
Re: [gmx-users] compilation error
yimnai forlemu wrote: Hello, I need some help figuring out how to compile gromacs on and sgi or linux machine. This is the error I get after using the make command to compile gromacs. Need some suggestions. Thanks What compiler and compiler version are you using? It looks archaic, from the error messages. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
