Re: [gmx-users] g_angle gets confused by switching default output file names.
[EMAIL PROTECTED] wrote: g_angle -ov angaver.xvg :: yields average angle g_angle -ov angdist.xvg :: yields angle distribution My Gromacs-3.3 command was: g_angle -ov x.xvg -type dihedral -f traj.xtc -s topol.tpr -n my.ndx Easily avoided, just posting a notice. ' OK, maybe the program is a bit braindead but actually none of the gromacs programs checks for double filenames. If you check your directory you'll find a backup file #angdist.xvg.1# with the average angle as well as angdist.xvg with the distribution. The average is written first, then the file is backuped and the distribution is written. ___ 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
Re: [gmx-users] topology transformation
Anthony Cruz wrote: Hi users: How I can convert a topology generated by PRODRG topology generation server to a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 Forcefield There is no automatic way to do that. You'll have to assign Gromos atom types (which are similar to those from ProDrg, but *not* identical!) and bonded types (for bonds, angles, dihdedrals and impropers). You may have to check (or add) the exclusions also. You could use my 'Topology Tools' (see contributions section) to make life easier. After you assign atom types, you use nr2nametop to change all atom numbers into labels that include the atom names and types. Then, e.g., bonds in your itp file will look like: [bonds] CA(CH3) C(C) parameters C(C) O(O) parameters Then, using the comments in the ffG43a1bon.itp file, like: #define gb_40.1230 1.6600e+07 ; C - O1200 you can easily guess to assign gb_4 to the second bond. And, yes, it would be possible to automate this to some extent, but it woulc be dangerous, too. Assigning bonded interactions like this is really guesswork, you will have a good starting point for a molecular topology, but (important and/or crucial) details may be horribly wrong. In practice, it usually works very well, though... -- Groetjes, Anton * NOTE: New Affiliation, Phone Fax numbers (below) * _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ | | | If You See Me Getting High, Knock Me Down (RHCP)| |_|___| ___ 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] ligand falling out of active site during EM
Diane Fournier wrote: Thank you ! I think the problem was indeed with building the box, because I redid the whole sequence on my drug-enzyme system (building the box with editconf, putting the water with genbox, and then writing my .tpr file with grompp) and ran the same (test) position restraint md run, and this time, the ligand was inside. Will try minimisation again. For the record: you have almost certainly had problems with PBC. mdrun will always place molecules 'in the box' (see manual). If your complex happens to be on the box edge, one molecule may end up at a different side of the box. If, instead, your complex was in the middle of the box, as probably happend during your second setup sequence, pbc will not affect it, at least not during EM when molecules tend not to move much. Note, that for different box shapes, the 'middle of the box' may not be what you expect. -- Groetjes, Anton * NOTE: New Affiliation, Phone Fax numbers (below) * _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ | | | If You See Me Getting High, Knock Me Down (RHCP)| |_|___| ___ 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] ligand falling out of active site during EM
Hi, Maybe as a note for any interested but unaware. In gromacs, the middle of the box is always the middle of the *rectangular* box defined by the first three numbers in the last line of the .gro file. Cheers, Tsjerk On 5/9/06, Anton Feenstra [EMAIL PROTECTED] wrote: Diane Fournier wrote: Thank you ! I think the problem was indeed with building the box, because I redid the whole sequence on my drug-enzyme system (building the box with editconf, putting the water with genbox, and then writing my .tpr file with grompp) and ran the same (test) position restraint md run, and this time, the ligand was inside. Will try minimisation again.For the record: you have almost certainly had problems with PBC. mdrun will always place molecules 'in the box' (see manual). If your complexhappens to be on the box edge, one molecule may end up at a differentside of the box.If, instead, your complex was in the middle of the box, as probably happend during your second setup sequence, pbc will not affect it, atleast not during EM when molecules tend not to move much.Note, that for different box shapes, the 'middle of the box' may not bewhat you expect. --Groetjes,Anton* NOTE: New Affiliation, Phone Fax numbers (below) *_ ___| | ||_ ,| K. Anton Feenstra || / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam ||( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands|| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ || | If You See Me Getting High, Knock Me Down (RHCP)||_|___|___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Getting out of the box!!!
Hello gmx users: I am running a very common MD simulation andthe protein system is getting OUT of the box after approximately 200 ps. I have tried several things. Does it happen very frequently? (common mistake) Is there any way to keep, during the whole calculation, the protein system into the center of the box? What could I do for avoiding this phenomenon? Thanks in advance. Marcelo ___ 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] Getting out of the box!!!
Marcelo, Have you considered reading the FAQ, searching the mailing list, reading the manual or just paying attention? Just yesterday there was mention of a ligand jumping out of the box, to which several replies were given and your exact question is asked on this list at least every month! I'll keep my temper. It's just due to the periodic boundary conditions, nothing wrong, you can use trjconv with option -pbc nojump afterwards or you can set comm_mode to linear with the protein as comm_group. Now please read the manual on periodic boundary conditions and for further reference search the mail list (e.g. periodic boundary conditions, PBC, jumping, etc...) TsjerkOn 5/10/06, Marcelo Fabricio Masman [EMAIL PROTECTED] wrote: Hello gmx users: I am running a very common MD simulation andthe protein system is getting OUT of the box after approximately 200 ps. I have tried several things. Does it happen very frequently? (common mistake) Is there any way to keep, during the whole calculation, the protein system into the center of the box? What could I do for avoiding this phenomenon? Thanks in advance. Marcelo ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Getting out of the box!!!
Thank you very much foryour recommendations, Tsjerk. Marcelo On 5/10/06, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Marcelo,Have you considered reading the FAQ, searching the mailing list, reading the manual or just paying attention? Just yesterday there was mention of a ligand jumping out of the box, to which several replies were given and your exact question is asked on this list at least every month! I'll keep my temper. It's just due to the periodic boundary conditions, nothing wrong, you can use trjconv with option -pbc nojump afterwards or you can set comm_mode to linear with the protein as comm_group. Now please read the manual on periodic boundary conditions and for further reference search the mail list ( e.g. periodic boundary conditions, PBC, jumping, etc...)Tsjerk On 5/10/06, Marcelo Fabricio Masman [EMAIL PROTECTED] wrote: Hello gmx users: I am running a very common MD simulation andthe protein system is getting OUT of the box after approximately 200 ps. I have tried several things. Does it happen very frequently? (common mistake) Is there any way to keep, during the whole calculation, the protein system into the center of the box? What could I do for avoiding this phenomenon? Thanks in advance. Marcelo___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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: [gmx-users] Getting out of the box!!!
Tsjerk Wassenaar wrote: Marcelo, Have you considered reading the FAQ, searching the mailing list, reading the manual or just paying attention? Just yesterday there was mention of a ligand jumping out of the box, to which several replies were given and your exact question is asked on this list at least every month! Well, it is just possible Marcelo is new, Tsjerk... :-) I do echo your frustration from time to time that people don't display much initiative in solving their own problems, even to the point of not reading readily-available material in the manual. In general I'm happy to help someone, but I'm much happier to do so if I get the impression they're working actively to solve the problem, rather than doing an imitation of a sponge... after all, I'm giving up *my* time to help with someone else's problem that is of no consequence to me... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems in gromacs
Greeting gromacs users. I am trying to use gromacs to simulate metals. I am trying to simulate BCC Iron. But I get the following error message. Fatal error: Invalid order for directive moleculetype, file topol.top, line 5 I am sending you my input files. Please help me and tell me what is wrong with my files. Also can you tell me if it is possible to simulate metallic crystals using gromacs. Mostly people have worked on Bio Molecules. However I believe that I should be able to simulate Metallic structures if I modify the source codes a bit. Also, Can you please tell me if I can use my own potential functions? I downloaded force fields made by other people, I have modified them too to include xb_1 bond type and FE FE interaction. These modifications have been done in ffG53a6.rtp and ffG53a6bon.itp. These files are in 53a6.tar.gz on the force field download section of the website www.gromacs.org. I request you to please help me out as soon as you can. :) -- grompp.mdp NES STARTING WITH ';' ARE COMMENTS title = Minimization of Hen Egg White Lysozyme (1AKI.pdb) ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor include = -I../top ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 200 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps = Protein ; Which coordinate group(s) to write to disk energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = yes ; Periodic Boundary Conditions (yes/no) -- topol.top #include ffG53a6.itp ;#include ffgmx.rtp ;#include ffgmx.atp [ moleculetype ] Ions 3 [ atoms ] 1 Fe 1 HEME FE 1 0 55.870 2 Fe 2 HEME FE 1 0 55.870 3 Fe 3 HEME FE 1 0 55.870 4 Fe 4 HEME FE 2 0 55.870 5 Fe 5 HEME FE 2 0 55.870 6 Fe 6 HEME FE 2 0 55.870 7 Fe 7 HEME FE 2 0 55.870 8 Fe 8 HEME FE 3 0 55.870 9 Fe 9 HEME FE 3 0 55.870 [ bonds ] 1 2 1 0.1000 1.7800e+7 -- Pure Fe 9 1Fe FE 1 0.00 0.00 0.00 0.000 0.000 0.000 2Fe FE 2 2.70 0.00 0.00 0.000 0.000 0.000 3Fe FE 3 0.00 2.70 0.00 0.000 0.000 0.000 4Fe FE 4 0.00 0.00 2.70 0.000 0.000 0.000 5Fe FE 5 0.00 2.70 2.70 0.000 0.000 0.000 6Fe FE 6 2.70 0.00 2.70 0.000 0.000 0.000 7Fe FE 7 2.70 2.70 0.00 0.000 0.000 0.000 8Fe FE 8 2.70 2.70 2.70 0.000 0.000 0.000 9Fe FE 9 1.35 1.35 1.35 0.000 0.000 0.000 conf.gro ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems in gromacs
karamyog singh wrote: Greeting gromacs users. I am trying to use gromacs to simulate metals. I am trying to simulate BCC Iron. But I get the following error message. Fatal error: Invalid order for directive moleculetype, file topol.top, line 5 read chapter 5 in the manual about topology files. I am sending you my input files. Please help me and tell me what is wrong with my files. Also can you tell me if it is possible to simulate metallic crystals using gromacs. Mostly people have worked on Bio Molecules. However I believe that I should be able to simulate Metallic structures if I modify the source codes a bit. Also, Can you please tell me if I can use my own potential functions? Depends on what you want. CHeck manual on tabulated functions. I downloaded force fields made by other people, I have modified them too to include xb_1 bond type and FE FE interaction. These modifications have been done in ffG53a6.rtp and ffG53a6bon.itp. These files are in 53a6.tar.gz on the force field download section of the website www.gromacs.org http://www.gromacs.org. I request you to please help me out as soon as you can. :) -- grompp.mdp NES STARTING WITH ';' ARE COMMENTS title = Minimization of Hen Egg White Lysozyme (1AKI.pdb) ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor include = -I../top ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 200 ; Maximum number of (minimization) steps to perform nstenergy = 10; Write energies to disk every nstenergy steps nstxtcout = 10; Write coordinates to disk every nstxtcout steps xtc_grps= Protein ; Which coordinate group(s) to write to disk energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = yes ; Periodic Boundary Conditions (yes/no) -- topol.top #include ffG53a6.itp ;#include ffgmx.rtp ;#include ffgmx.atp [ moleculetype ] Ions 3 [ atoms ] 1 Fe 1HEME FE 1 055.870 2 Fe 2HEME FE 1 055.870 3 Fe 3HEME FE 1 055.870 4 Fe 4HEME FE 2 055.870 5 Fe 5HEME FE 2 055.870 6 Fe 6HEME FE 2 055.870 7 Fe 7HEME FE 2 055.870 8 Fe 8HEME FE 3 055.870 9 Fe 9HEME FE 3 055.870 [ bonds ] 1 2 1 0.1000 1.7800e+7 -- Pure Fe 9 1Fe FE1 0.00 0.00 0.00 0.000 0.000 0.000 2Fe FE2 2.70 0.00 0.00 0.000 0.000 0.000 3Fe FE3 0.00 2.70 0.00 0.000 0.000 0.000 4Fe FE4 0.00 0.00 2.70 0.000 0.000 0.000 5Fe FE5 0.00 2.70 2.70 0.000 0.000 0.000 6Fe FE6 2.70 0.00 2.70 0.000 0.000 0.000 7Fe FE7 2.70 2.70 0.00 0.000 0.000 0.000 8Fe FE8 2.70 2.70 2.70 0.000 0.000 0.000 9Fe FE9 1.35 1.35 1.35 0.000 0.000 0.000 conf.gro ___ 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]
Re: [gmx-users] Implementation of time-dependent Electric Field
Viswanadham Sridhara wrote: Hi everyone, This is regarding implementation of time-dependent electric field on the system. I tried looking into the manual, and did a bit of survey in mailing lists. I still dont know how to implement E_zt in .mdp options. As an example, can anyone tell me how to implement a 5ns E (V/nm) trapezoidal pulse (1ns rise and fall times with 3ns pulse on time). you can't. please check the source code, src/mdlib/sim_util.c Thanks in advance, -Viswanadham. -- Viswanadham Sridhara, Graduate Research Assistant, Old Dominion University, Norfolk, VA-23529. ___ 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] Value for bonded force constant (Kb)
Hi gmxions, Based on the litterature search , I am going to use Kb value of 4 Kcal/mol A2 (1673.6 KJ/mol nm2)as harmonic bonded force field constant(type 6) for restraining distance of Fe(II) ligated with atoms of 2 Nitrogen and 1 Oxygen. If any one having objection please correct me ): . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Value for bonded force constant (Kb)
Hi Raja,No objections from my side. But if you could also include the references resulting from your literature study, that would be nice to have in the archive (may save somebody searching the literature to find some iron - ligand parameters). Cheers,TsjerkOn 5/10/06, raja [EMAIL PROTECTED] wrote: Hi gmxions,Based on the litterature search , I am going to use Kbvalue of 4 Kcal/mol A2 (1673.6 KJ/mol nm2)as harmonic bonded forcefield constant(type 6) for restraining distance of Fe(II) ligated with atoms of 2 Nitrogenand1 Oxygen. If any one having objection pleasecorrect me ):.With thanks !B.Nataraj--raja[EMAIL PROTECTED] --http://www.fastmail.fm - Send your email first class___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulation of long chains in vacuum
Hello, gmx-users， i generated a chain of 1000 units and intended to simulate in vacuum, but the system exploded and the mdp file is as follows: title= PE cpp = /usr/bin/cpp include = define = integrator = md dt = 0.002 nsteps = 10 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy= 500 nstxtcout= 2000 xtc_grps = energygrps = comm_mode= angular nstlist = 0 ns_type = simple rlist= 0 rvdw = 0 rcoulomb = 0 pbc = no tcoupl = Berendsen tc-grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 4.5e-4 ;ref_p= 1.0 ;annealing = single ;annealing_npoints = 15 ;annealing_time = 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 ;annealing_temp = 370 365 360 355 350 345 340 335 330 325 320 315 310 305 300 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds optimize_fft = yes are there any obvious errors? and my system is quite large, about 49.90900 70.12100 231.85800 ns is there any upper limits for gromacs systems? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-05-10 ___ 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] Value for bonded force constant (Kb)
Hi Mr Tsjerkw, Thanks for your mail. Infact I intented to attach the reference link but I missed it. Anyway here is the link where I taken the value of Kb. Infact the reference only talk between Fe and O atoms. I belive this value will be more reasonably for my purpose. I will update the outcome of the result of MD using this restraints after my work completes. In mean time here is the reference link http://www.jbc.org/cgi/content/full/280/51/42188 For quick find out on the page , use this key work force constant of 4.0 kcal/mol/Å2 and please let me know the validity of my judgement. With Thanks ! B.Nataraj On Wed, 10 May 2006 13:50:17 +0200, Tsjerk Wassenaar [EMAIL PROTECTED] said: Hi Raja, No objections from my side. But if you could also include the references resulting from your literature study, that would be nice to have in the archive (may save somebody searching the literature to find some iron - ligand parameters). Cheers, Tsjerk On 5/10/06, raja [EMAIL PROTECTED] wrote: Hi gmxions, Based on the litterature search , I am going to use Kb value of 4 Kcal/mol A2 (1673.6 KJ/mol nm2)as harmonic bonded force field constant(type 6) for restraining distance of Fe(II) ligated with atoms of 2 Nitrogen and 1 Oxygen. If any one having objection please correct me ): . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ 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] Implementation of time-dependent Electric Field
Hi, On May 10, 2006, at 1:24 PM, David van der Spoel wrote: Viswanadham Sridhara wrote: Hi everyone, This is regarding implementation of time-dependent electric field on the system. I tried looking into the manual, and did a bit of survey in mailing lists. I still dont know how to implement E_zt in .mdp options. As an example, can anyone tell me how to implement a 5ns E (V/nm) trapezoidal pulse (1ns rise and fall times with 3ns pulse on time). you can't. please check the source code, src/mdlib/sim_util.c To clarify - the routine in question is called calc_f_el() and is _extremely_ simple, so you can probably implement it yourself with very little extra work. The coordinates of particule i (counting starts from 0, since we're using C) are available in units of nm in x[i][XX] x[i][YY] x[i][ZZ] Similarly, the forces you want to alter are in units of kJ/mol/nm, in f[i][XX] f[i][YY] f[i][ZZ] ... and the particle charge is charge[i], in electron charge units. So, go through all particles, check e.g. the z-coordinate and assign a field in V/nm based on this. We need to convert it to MD units too, so the force correction will be f[i][ZZ] += your_calculated_field_at_this_z_coordiate * FIELDFAC * charge[i]. Cheers, Erik ___ 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] simulation of long chains in vacuum
Rongliang Wu wrote: Hello, gmx-users， i generated a chain of 1000 units and intended to simulate in vacuum, but the system exploded and the mdp file is as follows: Please tell us you have done normal things like energy minimization and or position-restrained MD, and checked visually that things look OK else we might suspect the problem is that you haven't done these basic things and not bother wasting our time telling you to do them. are there any obvious errors? Looks OK to me. and my system is quite large, about 49.90900 70.12100 231.85800 ns is there any upper limits for gromacs systems? I don't believe so. You could look in the manual... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implementation of time-dependent Electric Field
Thanks for the quick feedback! On 5/10/06, Erik Lindahl [EMAIL PROTECTED] wrote: Hi,On May 10, 2006, at 1:24 PM, David van der Spoel wrote: Viswanadham Sridhara wrote: Hi everyone, This is regarding implementation of time-dependent electric field on the system. I tried looking into the manual, and did a bit of survey in mailing lists. I still dont know how to implement E_zt in .mdp options. As an example, can anyone tell me how to implement a 5ns E (V/nm) trapezoidal pulse (1ns rise and fall times with 3ns pulse on time). you can't. please check the source code, src/mdlib/sim_util.c To clarify - the routine in question is called calc_f_el() and is_extremely_ simple, so you can probably implement it yourself withvery little extra work.The coordinates of particule i (counting starts from 0, since we're using C) are available in units of nm inx[i][XX]x[i][YY]x[i][ZZ]Similarly, the forces you want to alter are in units of kJ/mol/nm, inf[i][XX]f[i][YY]f[i][ZZ]... and the particle charge is charge[i], in electron charge units. So, go through all particles, check e.g. the z-coordinate and assigna field in V/nm based on this. We need to convert it to MD units too,so the force correction will bef[i][ZZ] += your_calculated_field_at_this_z_coordiate * FIELDFAC * charge[i].Cheers,Erik___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Viswanadham Sridhara,Graduate Research Assistant, Old Dominion University,Norfolk, VA-23529. ___ 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] topology transformation
Anthony Cruz wrote: Hi users: Hi Anthony, How I can convert a topology generated by PRODRG topology generation server to a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 Forcefield did you try the beta version? It generates 43A1 topologies. There are some issues with impropers and atom types in phosphate groups (see my comment on this list a few months ago), but everything else IMHO is parameterized very well. The charges sometimes aren't polar enough (e.g. in hydroxyl groups), thus you should use standard 43A1 charge group charges as far as possible. For unknown moieties you may need to do some QM calculations (e.g. DFT/ESP). Regards Christian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How many ps needs a simulation?
How many ps needs a simulation? How long is a piece of string? Seriously though, depends on what you are trying to observe and determine. Also check the literature to see what is currently being done with similar systems and properties. Typically it will be at least an order of magnitude longer than the process you wish to observe. But what is possible and what you want can be very too different things. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] How many ps needs a simulation?
Thanks, In fact I have a sequence with 1277 residue. It is stable even in 50ps. But when I continue to simulation my pc is restarted in 4 steps, automaticly. I should say that this step needs about 100 h time."Dallas B. Warren" [EMAIL PROTECTED] wrote: How many ps needs a simulation?How long is a piece of string?Seriously though, depends on what you are trying to observe anddetermine.Also check the literature to see what is currently being done withsimilar systems and properties."Typically" it will be at least an order of magnitude longer than theprocess you wish to observe. But what is possible and what you want canbe very too different things.Catch ya,Dr. Dallas WarrenLecturerDepartment of Pharmaceutical Biology and PharmacologyVictorian College of Pharmacy, Monash University381 Royal Parade, Parkville VIC 3010[EMAIL PROTECTED]+61 3 9903 9524-When the only tool you own is a hammer, every problem begins to resemblea nail. ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.___ 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
