[gmx-users] Dihedral restraints
Hello All, While doing NMR refinement or custom force addition, it can happen than the force on the system can push the peptide plane atoms out of the plane. [ like the amide bond is pushed out of the plane to satisfy the external force or the omega angle is deformed beyond acceptable values]. To control this behavior, I want to employ dihedral restrains on my system. I have understood the format and the required steps but the results of a short simulation are not as expected. For example : #18 : C of resid 1 ; 20 : N of resid 2 ; 5 : CA of resid 1 ; 22 : CA of resid 2 # 19 : O of resid 1 ; 21 : H of resid 2. #; ai ajakal type label phi dphi kfac power 5 18 20 22 1 0 180.00 4 1 1 19 18 20 22 1 0 0.004 1 1 5 18 20 21 1 0 180.00 4 1 1 19 18 20 21 1 0 0.004 1 1 In the .mdp file, i have ;dihedral restraints dihre = yes dihre_fc= 50 ; or whatever value you desire nstdihreout = 50 I ran a short 2000 step simulation and over the period of time I tracked the four dihedral values, every row is a timestep. #the first line is the restrained reference value. 180 0 180 0 -147.287215895064 9.45865329024718-159.203988508429 -2.45811932311724 -111.050389450397 -81.9953887566147 -92.0822326476887 -63.0272319539059 -110.958596230868 -73.8376501933164 -92.9130172813275 -55.7920712437757 -112.517830994369 -59.5426717504823 -102.604122568900 -49.6289633250131 -100.996135584400 -74.4228693635875 -87.2297061267471 -60.6564399059348 -93.9669086707340 -57.7658765173159 -86.3382092652599 -50.1371771118417 -95.0591618723864 -66.9832558152160 -85.0934054990846 -57.0174994419143 -94.2190629339560 -52.6947808390542 -91.1562898592925 -49.6320077643907 -87.5354914279667 -69.2330638322494 -73.2840411103266 -54.9816135146093 -112.405078265351 -73.0596345313864 -97.4992184521689 -58.1537747182041 As you can see, the value moves away from the reference value as the simulation goes on. Any hints about any possible mistake in my implementation would be appreciated. Thanks Santhosh -- View this message in context: http://gromacs.5086.n6.nabble.com/Dihedral-restraints-tp5006617.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X
Thanks - I have filed issue #1194 and assigned it to David. http://redmine.gromacs.org/issues/1194 Let me know if there is anything else that is needed. I could take a shot at myself, and will play around with it, but I don't know the details of the symtab in any detail, unfortunately. 15 mar 2013 kl. 19:51 skrev David van der Spoel: Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? redmine please. Thanks /Per-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Dihedral restraints in 4.6 vs 4.5.X
Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral restraint. Here's the details: Making a 4.5.5 tpr with a dihedral restraint $grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr Checking that it is there: $gmxdump -s md.tpr |grep DIHRE Reading file md.tpr, VERSION 4.5.5 (single precision) functype[166]=DIHRES, label=0, power= 1 phi= 1.2000e+02, dphi= 3.e+01, kfac= 1.e+00) Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives me an error. $ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md Reading file md.tpr, VERSION 4.5.5 (single precision) --- Program mdrun, VERSION 4.6.1 Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136 Fatal error: symtab get_symtab_handle 1051260126 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? Thanks /Per-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X
On 2013-03-15 15:31, Per Larsson wrote: Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral restraint. Here's the details: Making a 4.5.5 tpr with a dihedral restraint $grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr Checking that it is there: $gmxdump -s md.tpr |grep DIHRE Reading file md.tpr, VERSION 4.5.5 (single precision) functype[166]=DIHRES, label=0, power= 1 phi= 1.2000e+02, dphi= 3.e+01, kfac= 1.e+00) Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives me an error. $ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md Reading file md.tpr, VERSION 4.5.5 (single precision) --- Program mdrun, VERSION 4.6.1 Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136 Fatal error: symtab get_symtab_handle 1051260126 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? redmine please. Thanks /Per-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Dihedral restraints
Hi, I tried restraining two residues of my peptide . The restraints were added after dihedrals in the top file. Here's how the .top file looks : [ dihedrals ] ; aiajakal functc0c1 c2c3 16 41817 2 18162019 2 25222726 2 25272226 2 27252928 2 27252829 2 30203231 2 32303433 2 37343938 2 39374140 2 48465049 2 48504649 2 50485251 2 50524851 2 52475053 2 52504753 2 54415655 2 [ dihedral_restraints ] ; ai ajakal type label phi dphi kfac power ; phi C'(n-1) - N - CA - C' 16 18 2030 1 1 -60 0 5 2 ; psi N - CA - C' - N(n+1) 18 2030 32 1 1 -30 0 5 2 ; phi C'(n-1) - N - CA - C' 30 32 3437 1 1 -90 0 5 2 ; psi N - CA - C' - N(n+1) 323437 39 17 1 1 0 0 5 2 I am getting the following error when I used the grompp command :- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 4, expected 5 or 5 for Dih. Rest.. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You Fill Your Space So Sweet (F. Apple) Where did I do the mistake , can anybody guide me in this regard ?? , Also I don't know what should be the value for power and kfac , what I need is that the angles should be restrained to what I mentioned in file. Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Dihedral restraints
Hi, I tried restraining two residues of my peptide . The restraints were added after dihedrals in the top file. Here's how the .top file looks : [ dihedrals ] ; aiajakal functc0c1 c2c3 16 41817 2 18162019 2 25222726 2 25272226 2 27252928 2 27252829 2 30203231 2 32303433 2 37343938 2 39374140 2 48465049 2 48504649 2 50485251 2 50524851 2 52475053 2 52504753 2 54415655 2 [ dihedral_restraints ] ; ai ajakal type label phi dphi kfac power ; phi C'(n-1) - N - CA - C' 16 18 2030 1 1 -60 0 5 2 ; psi N - CA - C' - N(n+1) 18 2030 32 1 1 -30 0 5 2 ; phi C'(n-1) - N - CA - C' 30 32 3437 1 1 -90 0 5 2 ; psi N - CA - C' - N(n+1) 323437 39 17 1 1 0 0 5 2 I am getting the following error when I used the grompp command :- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 4, expected 5 or 5 for Dih. Rest.. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You Fill Your Space So Sweet (F. Apple) Where did I do the mistake , can anybody guide me in this regard ?? , Also I don't know what should be the value for power and kfac , what I need is that the angles should be restrained to what I mentioned in file. Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] dihedral restraints documentation
Just a note concerning dihedral restraints documentation -- the function and default behavior of dihre-fc needs to be documented somewhere in the manual. I just spent a couple hours (and my student a couple of days!) trying to track down the source of some crashes which ended up being due to the difference between specifying dihre-fc = 1 in our topology file, and not specifying anything at all. THis how-to documents what dihre-fc DOES ( http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints) but it is not mentioned anywhere in the gromacs manual at all. It turns out dihre-fc defaults to 1000, so the difference between dihre-fc = 1 and omitting dihre-fc is a factor of 1000 in dihedral restraint strength. This is enough (since it's a multiplier!) to make the difference between simulations reliably crashing and simulations not crashing at all... This clearly should be documented in the manual since (with this behavior) knowing what value of dihre-fc one is using is critical to knowing what dihedral restraint strength one is using. Thanks. -- David Mobley dmob...@gmail.com 504-383-3662 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dihedral Restraints
The piece of code in dihres.c does it right (at least for the energy I would say... can't say anything about the force)... but the equation in the manual is wrong or at least misleading. On 05/03/11, Sai Pooja saipo...@gmail.com wrote: Hi, In Manual 4.5.3, the potential for dihedral restraints is the following: Phi* = (Phi - Phi0)MOD 2Pi Where Phi is the instantaneous dihedral and Phi0 is the reference dihedral. And the MOD2Pi, I assume, ensures a difference 2Pi. The Potential is: V=0.5*K*(Phi* - Phi0 -deltaPhi)**2 for all Phi* deltaPhi and so on ... I am just confused if this is just a typo? Why are we subtracting Phi0 TWICE?? There's an outstanding Redmine issue on this topic - http://redmine.gromacs.org/issues/597. Please contribute anything useful. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Dihedral Restraints
Hi, In Manual 4.5.3, the potential for dihedral restraints is the following: Phi* = (Phi - Phi0)MOD 2Pi Where Phi is the instantaneous dihedral and Phi0 is the reference dihedral. And the MOD2Pi, I assume, ensures a difference 2Pi. The Potential is: V=0.5*K*(Phi* - Phi0 -deltaPhi)**2 for all Phi* deltaPhi and so on ... I am just confused if this is just a typo? Why are we subtracting Phi0 TWICE?? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dihedral Restraints
On 05/03/11, Sai Pooja saipo...@gmail.com wrote: Hi, In Manual 4.5.3, the potential for dihedral restraints is the following: Phi* = (Phi - Phi0)MOD 2Pi Where Phi is the instantaneous dihedral and Phi0 is the reference dihedral. And the MOD2Pi, I assume, ensures a difference 2Pi. The Potential is: V=0.5*K*(Phi* - Phi0 -deltaPhi)**2 for all Phi* deltaPhi and so on ... I am just confused if this is just a typo? Why are we subtracting Phi0 TWICE?? There's an outstanding Redmine issue on this topic - http://redmine.gromacs.org/issues/597. Please contribute anything useful. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] dihedral restraints in gromacs 4.0.5
Steven Ari Beasley wrote: has anyone successfully incorporated dihedral angle restraints in gromacs 4.0.5 protein simulation. i can only find instructions for gromacs 3.3.1, nothing in the manual. Do these instructions not work? http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints i don't know if the format is the same or whether it requires diffent .mdp flags, but so far i have not been able to successfully run a I don't believe there have been any changes as far as .mdp keywords (dihre_tau might be ignored, but I can't remember at the moment). If you post what you're trying and any errors that you receive or evidence that the restraints are not working, that would be useful in providing assistance. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints wiki section
Dear chris, Thank you for your help about performing dihedral restraints. Would you please kindly explain to me how I can measure the value of dihedral angles between two amin acids (I mean C'-N-C-C' and N-C-C'-N). Thank you in advance for your valuable aid. Behnoush - Original Message - From: chris neale [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran Subject: [gmx-users] dihedral restraints wiki section I have added a section on dihedral restraints to the wiki. http://wiki.gromacs.org/index.php/Dihedral_Restraints ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints wiki section
Thank you for your help about performing dihedral restraints. Would you please kindly explain to me how I can measure the value of dihedral angles between two amin acids (I mean C'-N-C-C' and N-C-C'-N). Thank you in advance for your valuable aid. Well this should really be easy to find out! check out the manual, there is section ANALYSIS ... g_angle is one option. Behnoush - Original Message - From: chris neale [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran Subject: [gmx-users] dihedral restraints wiki section I have added a section on dihedral restraints to the wiki. http://wiki.gromacs.org/index.php/Dihedral_Restraints ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints wiki section
Behnoush Zare wrote: Dear xavier, Thank you for your reply bur I want to run md simulation with regarding dihedral restraints on helices. According to the chris suggestion I should add the dihedral values of the helices backbone to the .top file. My question is about calculating of dihedral angles values. Any help would be appreciated. If you're after canonical values for backbone dihedral angles in helices, then you should check out some textbook material, or survey some representative structures in the PDB and measure them there. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints wiki section
Dear xavier, Thank you for your reply bur I want to run md simulation with regarding dihedral restraints on helices. According to the chris suggestion I should add the dihedral values of the helices backbone to the .top file. My question is about calculating of dihedral angles values. Any help would be appreciated. Behnoush - Original Message - From: Xavier Periole [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, January 29, 2008 1:17:45 PM (GMT+0330) Asia/Tehran Subject: Re: [gmx-users] dihedral restraints wiki section Thank you for your help about performing dihedral restraints. Would you please kindly explain to me how I can measure the value of dihedral angles between two amin acids (I mean C'-N-C-C' and N-C-C'-N). Thank you in advance for your valuable aid. Well this should really be easy to find out! check out the manual, there is section ANALYSIS ... g_angle is one option. Behnoush - Original Message - From: chris neale [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran Subject: [gmx-users] dihedral restraints wiki section I have added a section on dihedral restraints to the wiki. http://wiki.gromacs.org/index.php/Dihedral_Restraints ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral restraints
Behnoush Zare wrote: Dear chris, According to your note about dihedral restraints, how I can calculate the torsional angles of the helix backbone. I performed it using Deepview but it took long time. I think there should be more feasible one. Behnoush, So far your use of measure and calculate with regard to dihedral angles has been vague. I can't tell if you're trying to determine what these angles should be restrained to, determine what they are in your starting structure, or something else. Either way, the calculation is trivial. You should also have the courtesy to reply to the two people who've made suggestions for you, letting them know whether they've been successful in working out what you want. Otherwise, people may notice this and decide you're not worth their time :-) 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral restraints
Dear Mark, Ofcourse I'm worth your and others time since I reffered to some text and gromacs manuals as you and xavier suggest to me and I'm very appreciated. But I didn't give any clue. After all I try to be more precise about the replies. Behnoush - Original Message - From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 30, 2008 1:47:20 AM (GMT+0330) Asia/Tehran Subject: Re: [gmx-users] Dihedral restraints Behnoush Zare wrote: Dear chris, According to your note about dihedral restraints, how I can calculate the torsional angles of the helix backbone. I performed it using Deepview but it took long time. I think there should be more feasible one. Behnoush, So far your use of measure and calculate with regard to dihedral angles has been vague. I can't tell if you're trying to determine what these angles should be restrained to, determine what they are in your starting structure, or something else. Either way, the calculation is trivial. You should also have the courtesy to reply to the two people who've made suggestions for you, letting them know whether they've been successful in working out what you want. Otherwise, people may notice this and decide you're not worth their time :-) 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral restraints
If I understand what you're trying to do correctly, you want to measure the dihedral of some given sequence of backbone atoms in your peptide and restrain this angle to the starting value. Is that much correct? I've gotten lost a bit in this thread as to your intent, and as Mark pointed out, it's getting difficult to follow. If that is indeed the case, then Xavier gave you the answer already. Use g_angle on your starting structure, using an index group that specifies the appropriate atoms. The manual has clear explanations on how to do this measurement. I performed a similar calculation on an arbitrary structure I had around and it worked in less than 2 seconds. -Justin Quoting Behnoush Zare [EMAIL PROTECTED]: Dear Mark, Ofcourse I'm worth your and others time since I reffered to some text and gromacs manuals as you and xavier suggest to me and I'm very appreciated. But I didn't give any clue. After all I try to be more precise about the replies. Behnoush - Original Message - From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 30, 2008 1:47:20 AM (GMT+0330) Asia/Tehran Subject: Re: [gmx-users] Dihedral restraints Behnoush Zare wrote: Dear chris, According to your note about dihedral restraints, how I can calculate the torsional angles of the helix backbone. I performed it using Deepview but it took long time. I think there should be more feasible one. Behnoush, So far your use of measure and calculate with regard to dihedral angles has been vague. I can't tell if you're trying to determine what these angles should be restrained to, determine what they are in your starting structure, or something else. Either way, the calculation is trivial. You should also have the courtesy to reply to the two people who've made suggestions for you, letting them know whether they've been successful in working out what you want. Otherwise, people may notice this and decide you're not worth their time :-) 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dihedral restraints wiki section
Ofcourse I'm worth your and others time since I reffered to some text and gromacs manuals as you and xavier suggest to me and I'm very appreciated. But I didn't give any clue. After all I try to be more precise about the replies. The best way to return the favour is to post a message back to the list detailing what happened when you attempted their suggestion. Replies such as your suggestion didn't work are not helpful. It would be much more useful to say I tried g_angle by using the following command: (list exact command) but it produced X when what I want is Y. Perhaps the gromacs wiki could benefit from a page outlining some tips for using the mailing list. Behnoush Behnoush Zare wrote: / Dear chris, // // According to your note about dihedral restraints, how I can calculate the torsional angles of the helix backbone. I performed it using Deepview but it took long time. I think there should be more feasible one. / Behnoush, So far your use of measure and calculate with regard to dihedral angles has been vague. I can't tell if you're trying to determine what these angles should be restrained to, determine what they are in your starting structure, or something else. Either way, the calculation is trivial. You should also have the courtesy to reply to the two people who've made suggestions for you, letting them know whether they've been successful in working out what you want. Otherwise, people may notice this and decide you're not worth their time :-) 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints wiki section
Chris Neale wrote: Ofcourse I'm worth your and others time since I reffered to some text and gromacs manuals as you and xavier suggest to me and I'm very appreciated. But I didn't give any clue. After all I try to be more precise about the replies. The best way to return the favour is to post a message back to the list detailing what happened when you attempted their suggestion. Replies such as your suggestion didn't work are not helpful. It would be much more useful to say I tried g_angle by using the following command: (list exact command) but it produced X when what I want is Y. Perhaps the gromacs wiki could benefit from a page outlining some tips for using the mailing list. We have one here... http://wiki.gromacs.org/index.php/Support Obviously, feel free to expand! 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral restraints
Thank you Justin. I tried with g_angle and it worked.It gave me some .xvg files such as angdist.xvg , angaver.xvg ,dihfrac.xvg ot dihtrans.xvg and I should read the manual more carefully and analyze the outputs. Thank you again for your patience. Behnoush - Original Message - From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 30, 2008 2:43:49 AM (GMT+0330) Asia/Tehran Subject: Re: [gmx-users] Dihedral restraints If I understand what you're trying to do correctly, you want to measure the dihedral of some given sequence of backbone atoms in your peptide and restrain this angle to the starting value. Is that much correct? I've gotten lost a bit in this thread as to your intent, and as Mark pointed out, it's getting difficult to follow. If that is indeed the case, then Xavier gave you the answer already. Use g_angle on your starting structure, using an index group that specifies the appropriate atoms. The manual has clear explanations on how to do this measurement. I performed a similar calculation on an arbitrary structure I had around and it worked in less than 2 seconds. -Justin Quoting Behnoush Zare [EMAIL PROTECTED]: Dear Mark, Ofcourse I'm worth your and others time since I reffered to some text and gromacs manuals as you and xavier suggest to me and I'm very appreciated. But I didn't give any clue. After all I try to be more precise about the replies. Behnoush - Original Message - From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 30, 2008 1:47:20 AM (GMT+0330) Asia/Tehran Subject: Re: [gmx-users] Dihedral restraints Behnoush Zare wrote: Dear chris, According to your note about dihedral restraints, how I can calculate the torsional angles of the helix backbone. I performed it using Deepview but it took long time. I think there should be more feasible one. Behnoush, So far your use of measure and calculate with regard to dihedral angles has been vague. I can't tell if you're trying to determine what these angles should be restrained to, determine what they are in your starting structure, or something else. Either way, the calculation is trivial. You should also have the courtesy to reply to the two people who've made suggestions for you, letting them know whether they've been successful in working out what you want. Otherwise, people may notice this and decide you're not worth their time :-) 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken)
Chris, At one point the forces were incorrrect in the dihedral restraints. I *think* this was in 3.3 but one of the developers will probably know. I have a note to this effect in one of my publications too but I haven't the time to find it right now. David On Jan 26, 2008 10:43 PM, [EMAIL PROTECTED] wrote: This is just a notice for the archives. I was recently working on a new cluster where only gromacs 3.3 is installed. It took me a while to figure out that the [ dihedral_restraints ] section is either differently implemented or broken in 3.3 compared to 3.3.1. Since the online list of revisions is not up to date past 3.2, I thought I would put a note on the mailing list. There is some discussion about versions and dihedral restraints here: http://www.gromacs.org/pipermail/gmx-users/2006-March/020512.html And for using dihedral restraints in 3.3.1, a description is here: http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken)
Dear Dr. Neale, I try to perform dihedral_restraints on protein helices. Searching on this subject in the gromacs manual, wiki.gromacs and gmx-mailing list give me some clue but it is not clear for me yet. Also I did some you suggest in following address: http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html In my top file I added lines below and include all the atoms in the helices in case of A,B,C,D: [ dihedral_restraints ] ; ai ajakal type label phi psi dphi kfac power AB C D1 1180 180 0 1 2 And in the mdp file I include these lines: ;dihedral restraints dihre = simple dihre_fc= 100 dihre_tau = 0.0 nstdihreout = 50 But I have got error in processing the top file. Fatal error: Ther were 1 error(s) processing your input I have referred to the manual and not found any thing about dihedral_restraints details. Would you please explain to me what I should do. Thank you very much in advance for your kindness and expertize. Best regards Behnoush - Original Message - From: chris neale [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Sunday, January 27, 2008 10:13:42 AM (GMT+0330) Asia/Tehran Subject: [gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken) This is just a notice for the archives. I was recently working on a new cluster where only gromacs 3.3 is installed. It took me a while to figure out that the [ dihedral_restraints ] section is either differently implemented or broken in 3.3 compared to 3.3.1. Since the online list of revisions is not up to date past 3.2, I thought I would put a note on the mailing list. There is some discussion about versions and dihedral restraints here: http://www.gromacs.org/pipermail/gmx-users/2006-March/020512.html And for using dihedral restraints in 3.3.1, a description is here: http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dihedral restraints wiki section
I have added a section on dihedral restraints to the wiki. http://wiki.gromacs.org/index.php/Dihedral_Restraints ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken)
This is just a notice for the archives. I was recently working on a new cluster where only gromacs 3.3 is installed. It took me a while to figure out that the [ dihedral_restraints ] section is either differently implemented or broken in 3.3 compared to 3.3.1. Since the online list of revisions is not up to date past 3.2, I thought I would put a note on the mailing list. There is some discussion about versions and dihedral restraints here: http://www.gromacs.org/pipermail/gmx-users/2006-March/020512.html And for using dihedral restraints in 3.3.1, a description is here: http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
R: R: [gmx-users] Dihedral restraints
Dear David I am desperate actually and would appreciate a lot if you could send me the dihres.c that works with version 3.2. Just in case is not so clear how to add the right lines in the topology file by reading the code would you please suggest it to me too? Thanks a lot Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] Tel: +39-02-64433097 -Messaggio originale- Da: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Per conto di David Mobley Inviato: giovedì 16 marzo 2006 0.59 A: Discussion list for GROMACS users Oggetto: Re: R: [gmx-users] Dihedral restraints Regarding dihedral restraints in 3.2, the dihres.c section of code only was a placeholder in 3.2 (it printed out dihedral restraints on but the dihedral restraints did nothing) but was fixed (sort of) before release of 3.3. I think the forces were still wrong in t he 3.3 release, though, so even if you get 3.3 working, you will probably need to get the fixed dihres.c. I do, however, probably have a dihres.c floating around somewhere that would work properly with 3.3, and possibly also with 3.2 (at one point David van der Spoel wrote the section of code after I discovered it was missing from the 3.2 release). If you are desperate I can dig around for it. Thanks, David On 3/15/06, David van der Spoel [EMAIL PROTECTED] wrote: STEVENAZZI ANDREA wrote: Dear David I did check the mailing list archives and could not find anything related to. Moreover, I have experienced some problems with version 3.3 of Gromacs related to PME (see the mailing list archives) and I was forced to install the 3.2.1 version in order to run a simulation. There is a workaround for this too on the ftp site. So you are telling me that dihedral restraints can not be set up in the 3.2 version? Don't recall but probably not. I beg you pardon if these are stupid questions, but I have started to use Gromacs just 2 weeks ago. Thanks Andrea STEVENAZZI ANDREA wrote: Dear Gromacs Users I am trying to use Gromacs for the MD of a small modified peptide (just 4 residues with one ethylated) and I would like to set up one dihedral restraint in the topology file. I have not found anything useful on the paper manual regarding dihedral restraints and thought that it might not be possible to set them. However, analysing the mdout.mdp file I realised that the keyword dihre (dihedral angle restraints) is actually there and can be turned on. If that is true, does anybody know the right lines to insert in the topology file in order to set properly a dihedral restraints? Thanks manual is a bit outdated. check mailing list archives. it is possible with 3.3 Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Tel: +39-02-64433097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: R: R: [gmx-users] Dihedral restraints
You may consider to use following to get the latest 3.3. cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx Yang Ye STEVENAZZI ANDREA wrote: Dear David I am desperate actually and would appreciate a lot if you could send me the dihres.c that works with version 3.2. Just in case is not so clear how to add the right lines in the topology file by reading the code would you please suggest it to me too? Thanks a lot Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] Tel: +39-02-64433097 -Messaggio originale- Da: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Per conto di David Mobley Inviato: giovedì 16 marzo 2006 0.59 A: Discussion list for GROMACS users Oggetto: Re: R: [gmx-users] Dihedral restraints Regarding dihedral restraints in 3.2, the dihres.c section of code only was a placeholder in 3.2 (it printed out dihedral restraints on but the dihedral restraints did nothing) but was fixed (sort of) before release of 3.3. I think the forces were still wrong in t he 3.3 release, though, so even if you get 3.3 working, you will probably need to get the fixed dihres.c. I do, however, probably have a dihres.c floating around somewhere that would work properly with 3.3, and possibly also with 3.2 (at one point David van der Spoel wrote the section of code after I discovered it was missing from the 3.2 release). If you are desperate I can dig around for it. Thanks, David On 3/15/06, David van der Spoel [EMAIL PROTECTED] wrote: STEVENAZZI ANDREA wrote: Dear David I did check the mailing list archives and could not find anything related to. Moreover, I have experienced some problems with version 3.3 of Gromacs related to PME (see the mailing list archives) and I was forced to install the 3.2.1 version in order to run a simulation. There is a workaround for this too on the ftp site. So you are telling me that dihedral restraints can not be set up in the 3.2 version? Don't recall but probably not. I beg you pardon if these are stupid questions, but I have started to use Gromacs just 2 weeks ago. Thanks Andrea STEVENAZZI ANDREA wrote: Dear Gromacs Users I am trying to use Gromacs for the MD of a small modified peptide (just 4 residues with one ethylated) and I would like to set up one dihedral restraint in the topology file. I have not found anything useful on the paper manual regarding dihedral restraints and thought that it might not be possible to set them. However, analysing the mdout.mdp file I realised that the keyword dihre (dihedral angle restraints) is actually there and can be turned on. If that is true, does anybody know the right lines to insert in the topology file in order to set properly a dihedral restraints? Thanks manual is a bit outdated. check mailing list archives. it is possible with 3.3 Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Tel: +39-02-64433097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list
[gmx-users] Dihedral restraints
Dear Gromacs Users I am trying to use Gromacs for the MD of a small modified peptide (just 4 residues with one ethylated) and I would like to set up one dihedral restraint in the topology file. I have not found anything useful on the paper manual regarding dihedral restraints and thought that it might not be possible to set them. However, analysing the mdout.mdp file I realised that the keyword dihre (dihedral angle restraints) is actually there and can be turned on. If that is true, does anybody know the right lines to insert in the topology file in order to set properly a dihedral restraints? Thanks Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] Tel: +39-02-64433097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral restraints
STEVENAZZI ANDREA wrote: Dear Gromacs Users I am trying to use Gromacs for the MD of a small modified peptide (just 4 residues with one ethylated) and I would like to set up one dihedral restraint in the topology file. I have not found anything useful on the paper manual regarding dihedral restraints and thought that it might not be possible to set them. However, analysing the mdout.mdp file I realised that the keyword dihre (dihedral angle restraints) is actually there and can be turned on. If that is true, does anybody know the right lines to insert in the topology file in order to set properly a dihedral restraints? Thanks manual is a bit outdated. check mailing list archives. it is possible with 3.3 Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Tel: +39-02-64433097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
R: [gmx-users] Dihedral restraints
Dear David I did check the mailing list archives and could not find anything related to. Moreover, I have experienced some problems with version 3.3 of Gromacs related to PME (see the mailing list archives) and I was forced to install the 3.2.1 version in order to run a simulation. So you are telling me that dihedral restraints can not be set up in the 3.2 version? I beg you pardon if these are stupid questions, but I have started to use Gromacs just 2 weeks ago. Thanks Andrea STEVENAZZI ANDREA wrote: Dear Gromacs Users I am trying to use Gromacs for the MD of a small modified peptide (just 4 residues with one ethylated) and I would like to set up one dihedral restraint in the topology file. I have not found anything useful on the paper manual regarding dihedral restraints and thought that it might not be possible to set them. However, analysing the mdout.mdp file I realised that the keyword dihre (dihedral angle restraints) is actually there and can be turned on. If that is true, does anybody know the right lines to insert in the topology file in order to set properly a dihedral restraints? Thanks manual is a bit outdated. check mailing list archives. it is possible with 3.3 Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Tel: +39-02-64433097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: R: [gmx-users] Dihedral restraints
Regarding dihedral restraints in 3.2, the dihres.c section of code only was a placeholder in 3.2 (it printed out dihedral restraints on but the dihedral restraints did nothing) but was fixed (sort of) before release of 3.3. I think the forces were still wrong in t he 3.3 release, though, so even if you get 3.3 working, you will probably need to get the fixed dihres.c. I do, however, probably have a dihres.c floating around somewhere that would work properly with 3.3, and possibly also with 3.2 (at one point David van der Spoel wrote the section of code after I discovered it was missing from the 3.2 release). If you are desperate I can dig around for it. Thanks, David On 3/15/06, David van der Spoel [EMAIL PROTECTED] wrote: STEVENAZZI ANDREA wrote: Dear David I did check the mailing list archives and could not find anything related to. Moreover, I have experienced some problems with version 3.3 of Gromacs related to PME (see the mailing list archives) and I was forced to install the 3.2.1 version in order to run a simulation. There is a workaround for this too on the ftp site. So you are telling me that dihedral restraints can not be set up in the 3.2 version? Don't recall but probably not. I beg you pardon if these are stupid questions, but I have started to use Gromacs just 2 weeks ago. Thanks Andrea STEVENAZZI ANDREA wrote: Dear Gromacs Users I am trying to use Gromacs for the MD of a small modified peptide (just 4 residues with one ethylated) and I would like to set up one dihedral restraint in the topology file. I have not found anything useful on the paper manual regarding dihedral restraints and thought that it might not be possible to set them. However, analysing the mdout.mdp file I realised that the keyword dihre (dihedral angle restraints) is actually there and can be turned on. If that is true, does anybody know the right lines to insert in the topology file in order to set properly a dihedral restraints? Thanks manual is a bit outdated. check mailing list archives. it is possible with 3.3 Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Tel: +39-02-64433097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
