[gmx-users] About entropic contribution to the potential of mean force
Hi, In the manual of gromacs, the entropic contribution to the pmf is emphasized. In my opinion, this contribution is originated from the rotations of the constrained groups. However, according to the manual suggestion, "...when calculating a PMF between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed." I'm really confused with this. If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl- and many water molecules), I want to calculate the potential of mean force of NaCl, should I count the contributions from the entropic effects? According to Hess et al., (2006), JCP, 124: 164509, this effect should surely be added. So, any one experienced with similar researches can give me an answer for this: when should I add the entropic contribution to the pmfs? and, what the really physical explanation for this effect? Thanks in advance! Regards, zgzhang ___ 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] Using double precision files with single precision version
vivek sharma wrote: Hi All, I had a few MD runs with double precision in gromacs, Can I use single precision version of gromacs to play with those files e.g making movie files and extracting h_bond information. I am afraid if it will affect my results. I don't know whether it does work, but I suspect not. However it's trivial to compile a double-precision version, with --enable-double and --program-suffix=_d, and once installed you can use g_hbond when you want and g_hbond_d when you want. 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] Replacing molecules in .gro coordinate file
> > > Supposed I have a .gro file of 38 molecules of A which are already in > equilibrated conformations. Now I want to transform 15 molecules of A into B > therefore I will have the binary mixture of A/B with 13:15 molar ratio in > the final structure. How can I do this? Any suggestions will be appreciated. > Maybe open A & B in vmd together, and then save them as one PDB? Omer. ___ 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] Analyzing a trajectory split over multiple files
On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty <[EMAIL PROTECTED]>wrote: > Dear all, > > I have a very long trajectory split over a large number of files. What > would be the most efficient way to use the analysis programs over them? > Do they support multiple input for trajectory? Or I need to combine all > files into a single one anyway? > You should analyze each individual part on its own, and output the raw data of the result, then average the parts together. For example - say you are interested in coordination number of molecule X: For each part, output both the total number of X's found, plus the total number of X neighbors found. The coordination number is then the sum of neig. divided by the sum of X's, from ALL parts. It might be an issue if each part has different time length, then averaging the coordination number of each part might give more statistical weigh to short parts then they should have. In other words, you should first collect the data of each part together, and only then avg.. --Omer. ___ 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] Re: how to show dodecahedron box in VMD
Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: > Dear all: > > I am trying to show the dodecahedron box only in vmd since my simulation box > is dodecahedron. If I include water, I can see the box is dodecahedron. But > I want to get rid off all of water, then my box will not appear there. How > can I keep the dodecahedron box boundaries and solute only? Looks like only > the rectangular box boundaries can be drawn in VMD. > Does anyone has some suggestions? Appreciate your great help. > Happy Thanksgiving. > -Xianghong Qi > > -- > Some people make the world more special just by being in it. > > ___ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] List of all bonds form tpr file?
Hi, gmxdump in 4.0 still dumps all bonds. I don't know what causes you not to see them. Berk > Date: Wed, 26 Nov 2008 02:09:08 -0800 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] List of all bonds form tpr file? > > Dear All, > We have a script, which visualizes the bonds in the coarse-grained system > simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files > and extracted BONDS records. Now in 4.x it does not work because gmxdump no > longer outputs all bonds in the system. Is it possible to extract information > about *all* bonds in the system (not only the bonds in each moleculetype) > from tpr file in 4.x? > > Any help is appreciated! > > Semen > > > > > - Original Message > From: Mark Abraham <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Wednesday, November 19, 2008 1:57:19 PM > Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation? > > Semen Esilevsky wrote: > > Dear All, > > Where can I find documentation about the pull code in Gromacs 4.0? As far > > as I understand old style of setting up pulling simulations in separate > > file does not work any more, but I can't figure out how to transfer pulling > > params correctly to mdp file. Any help is appreciated! > > > > P.S. Probably the developers could put at least some very brief docs on web > > site while new manual is being prepared? Otherwise new cool features of 4.0 > > just can't be used by ordinary users... > > The beta manual is at ftp://ftp.gromacs.org/pub/beta/ > > 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] List of all bonds form tpr file?
I just realized that in 4.0 I modified things such that it only prints the bonds per molecule type. It would be quite easy to modify a program to write all bonds. (mk_angdx for instance). If you just have one atom type you can easily modify your script by reading the number of molecules and atoms_mol from the molblock print in the gmxdump output. Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] List of all bonds form tpr file? Date: Wed, 26 Nov 2008 11:52:45 +0100 Hi, gmxdump in 4.0 still dumps all bonds. I don't know what causes you not to see them. Berk > Date: Wed, 26 Nov 2008 02:09:08 -0800 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] List of all bonds form tpr file? > > Dear All, > We have a script, which visualizes the bonds in the coarse-grained system > simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files > and extracted BONDS records. Now in 4.x it does not work because gmxdump no > longer outputs all bonds in the system. Is it possible to extract information > about *all* bonds in the system (not only the bonds in each moleculetype) > from tpr file in 4.x? > > Any help is appreciated! > > Semen > > > > > - Original Message > From: Mark Abraham <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Wednesday, November 19, 2008 1:57:19 PM > Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation? > > Semen Esilevsky wrote: > > Dear All, > > Where can I find documentation about the pull code in Gromacs 4.0? As far > > as I understand old style of setting up pulling simulations in separate > > file does not work any more, but I can't figure out how to transfer pulling > > params correctly to mdp file. Any help is appreciated! > > > > P.S. Probably the developers could put at least some very brief docs on web > > site while new manual is being prepared? Otherwise new cool features of 4.0 > > just can't be used by ordinary users... > > The beta manual is at ftp://ftp.gromacs.org/pub/beta/ > > 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 Express yourself instantly with MSN Messenger! MSN Messenger _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: how to show dodecahedron box in VMD
Tsjerk Wassenaar ha scritto: Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: Dear all: I am trying to show the dodecahedron box only in vmd since my simulation box is dodecahedron. If I include water, I can see the box is dodecahedron. But I want to get rid off all of water, then my box will not appear there. How can I keep the dodecahedron box boundaries and solute only? Looks like only the rectangular box boundaries can be drawn in VMD. Does anyone has some suggestions? Appreciate your great help. Happy Thanksgiving. -Xianghong Qi -- Some people make the world more special just by being in it. ___ 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 Hi, you can try this: trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact* or trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1 well...the first converts all your trajectory and the last command extracts 1 frame in a gro file.. good luck alessandro ___ 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] Re: Loss of bonds in HEME iron after pdb2gmx
Justin A. Lemkul wrote: S and Fe atoms to be 0.25 +/- 0.2 nm apart. If they are much further Edit that: 0.25 nm +/- 0.02 nm. Apparently my math (and/or typing) skills are suspect first thing in the morning :) -Justin -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define
Hi, I also encoutered a strange behaviour of gmxcpp when using B-states. When I set up up a free energy simulation (gromacs 4.0.2) with amber03 (ffamber from Sorin & Pande), I define a dihedral angle, e.g. like [ dihedrals ] . 511 515 517 513 3 aromatic_prop_5aaromatic_prop_5 . If I process this topology with grompp it claims that there is no B-state defined. In the original ffamber03bon.itp there were comments in the define lines, e.g. #define aromatic_prop_5 41.84000 0.0 -41.84000 0.0 0.0 0.0 ; X-CR-NB-X (HIX) These were already removed since this causes grompp to cut the line after the first ";" and, hence it ignores the B-values. Now the strange thing: This works for all defined dihedrals except for those that end with an "a". So: 12 3 4 aromatic_prop_4 aromatic_prop_5 works fine, but 12 3 4 aromatic_prop_5a aromatic_prop_5 doesn't work. If I look into the processed topology, grompp has converted the first define, but not the second one. If I exchange the two dihedrals, like 12 3 4 aromatic_prop_5 aromatic_prop_5a it works again. I get the error only when these dihedrals are in the A-state: aromatic_prop_4a aromatic_prop_5a aromatic_prop_6a If I preprocess my topology with cpp -traditional all defines are nicely converted, so I guess there must go sth. wrong in gmxcpp. I also tried the fixed version from Berk as pointed out before, but this didn't do the job. Thanks, Daniel On Tuesday 25 November 2008 23:34:24 Berk Hess wrote: > Hi, > > That is an annoying bug. > I fixed it for 4.0.3. > If you want it fixed now, the diff is below. > > Berk > > > RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v > retrieving revision 1.9 > diff -r1.9 gmxcpp.c > 121,122c121,122 > < sscanf(define,"%s",name); > < ptr = define + strlen(name); > --- > > > sscanf(define,"%s%n",name,&i); > > ptr = define + i; > > > > > > Date: Tue, 25 Nov 2008 16:32:57 -0500 > > From: [EMAIL PROTECTED] > > To: gmx-users@gromacs.org > > Subject: [gmx-users] correct processing of #define statements by grompp > > in gromacs 4.0.2 requires exactly one space after #define > > > > When two spaces are included the #define KEYWORD is incompletely removed > > from the file. > > In case my conclusion about the exact nature of the error is incorrect, > > here is more information. > > > > I have a ffcharmbon.itp file that contains: > > > > [ dihedraltypes ] > > #define improper_NC2_X_X_C_ 180.0 83.68000 2 > > > > And an .itp file that contains: > > > > [ dihedrals ] > > 1 2 5 8 1 improper_NC2_X_X_C_ > > > > where grompp -pp returns > > > > [ dihedrals ] > > 1 2 5 8 1 _ 180.0 83.68000 2 > > > > and the floating '_' character causes the error message: > > > > ERROR 1 [file my.itp, line 77]: > > No default Proper Dih. types > > > > I tried to fix this by removing the trailing underscore character from > > my defined string in both files, > > but now I get a trailing 'C' > > > > [ dihedrals ] > > 1 2 5 8 1 C 180.0 83.68000 2 > > > > So it appears that the define statement is simply not being entirely > > removed. > > > > When I then replaced > > #define improper_NC2_X_X_C_ 180.0 83.68000 2 > > by > > #define improper_NC2_X_X_C_ 180.0 83.68000 2 > > (only one space between '#define' and 'improper...') > > it works correctly. > > > > Note that cpp handled this original define statement properly in gromacs > > 3.3.1. > > > > Chris. > > > > > > > > > > > > ___ > > 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 > > _ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen, Germany Tel: +49 551 201 2310 Fax: +49 551 201 2302 email: [EMAIL PROTECTED] www.mpibpc.mpg.de/groups/de_groot/dseelig/index.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] Problems with distance restraints
Hi all, I am trying to use a simple scheme to restrain a few distances within my protein, which is contained within an octahedral box of SPC water. In place of distance restraints, I'm using bond type 6 to utilize a harmonic potential to restrain the distance between a few atoms. When I imposed one such restraint in the topology, the simulation ran fine. After finishing this trajectory, I wanted to impose a second restraint and try again. At this point, the simulation fails with the following: mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt Initializing Domain Decomposition on 24 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 1.634 nm multi-body bonded interactions: 0.606 nm Minimum cell size due to bonded interactions: 1.797 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm Estimated maximum distance required for P-LINCS: 0.876 nm Guess for relative PME load: 0.45 Will use 12 particle-particle and 12 PME only nodes This is a guess, check the performance at the end of the log file Using 12 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm The maximum allowed number of cells is: X 2 Y 2 Z 2 --- Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2 Source code file: domdec.c, line: 5842 Fatal error: There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 2.24633 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- "I'm Only Faking When I Get It Right" (Soundgarden) I realize there are more optimizations I could impose to better balance the PP/PME load. I have tried those (altering my cutoff's and grid spacing) but it makes no difference. Plus, I'd like to remain consistent with the original simulation that used only one restraint. If I remove the second restraint, the simulation runs just fine. For reference, the restraints I'm imposing are: 330 1016 60.669 5.0300e+06 1016 559 60.376 5.0300e+06 The box vectors from the .gro file are: 7.14132 6.73290 5.83086 0.0 0.0 2.38044 0.0 -2.38044 3.36645 Is there anything obvious that I'm doing wrong? Or should I just use real distance restraints, according to manual section 4.3.4? Thanks for any insights. -Justin -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with distance restraints
Please disregard my message. I had a typo in my atom numbers that I was restraining. Apparently the distance between atoms 1016 and 559 is far greater than 0.376 nm, thus generating the error. -Justin Justin A. Lemkul wrote: Hi all, I am trying to use a simple scheme to restrain a few distances within my protein, which is contained within an octahedral box of SPC water. In place of distance restraints, I'm using bond type 6 to utilize a harmonic potential to restrain the distance between a few atoms. When I imposed one such restraint in the topology, the simulation ran fine. After finishing this trajectory, I wanted to impose a second restraint and try again. At this point, the simulation fails with the following: mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt Initializing Domain Decomposition on 24 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 1.634 nm multi-body bonded interactions: 0.606 nm Minimum cell size due to bonded interactions: 1.797 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm Estimated maximum distance required for P-LINCS: 0.876 nm Guess for relative PME load: 0.45 Will use 12 particle-particle and 12 PME only nodes This is a guess, check the performance at the end of the log file Using 12 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm The maximum allowed number of cells is: X 2 Y 2 Z 2 --- Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2 Source code file: domdec.c, line: 5842 Fatal error: There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 2.24633 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- "I'm Only Faking When I Get It Right" (Soundgarden) I realize there are more optimizations I could impose to better balance the PP/PME load. I have tried those (altering my cutoff's and grid spacing) but it makes no difference. Plus, I'd like to remain consistent with the original simulation that used only one restraint. If I remove the second restraint, the simulation runs just fine. For reference, the restraints I'm imposing are: 330 1016 60.669 5.0300e+06 1016 559 60.376 5.0300e+06 The box vectors from the .gro file are: 7.14132 6.73290 5.83086 0.0 0.0 2.38044 0.0 -2.38044 3.36645 Is there anything obvious that I'm doing wrong? Or should I just use real distance restraints, according to manual section 4.3.4? Thanks for any insights. -Justin -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx-users@gromacs.org
Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms->cU1 etc. These pointers will stay NULL when a user defined group is defined in the mdp file. I find these groups normally a pretty useful interface for simple fast implementations. 2) The pull code has indeed completely changed, however to me the questionable factor 0.5 remained the same: In pull.c: /* Add the pull contribution to the virial */ vir[j][m] += 0.5*f[j]*r_ij[g][m]; I do agree with the positive sign of the summation, but why is there a factor 0.5 to correct for double counting included in the summation. The summation is already ordered as r_ij and f[j] is the distance vector and force between the particle and the equilibrium position of the spring and therefore double counting cannot occur. Ofcourse it's possible that this factor 0.5 is not meant as a double counting correction factor, but then I don't see where it does come from. If this factor is indeed incorrect it might affect the pressure significantly in case a large pulling group is used. greetings Jelger ___ 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] Bugs in gromacs 4
Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms->cU1 etc. These pointers will stay NULL when a user defined group is defined in the mdp file. I find these groups normally a pretty useful interface for simple fast implementations. 2) The pull code has indeed completely changed, however to me the questionable factor 0.5 remained the same: In pull.c: /* Add the pull contribution to the virial */ vir[j][m] += 0.5*f[j]*r_ij[g][m]; I do agree with the positive sign of the summation, but why is there a factor 0.5 to correct for double counting included in the summation. The summation is already ordered as r_ij and f[j] is the distance vector and force between the particle and the equilibrium position of the spring and therefore double counting cannot occur. Ofcourse it's possible that this factor 0.5 is not meant as a double counting correction factor, but then I don't see where it does come from. If this factor is indeed incorrect it might affect the pressure significantly in case a large pulling group is used. greetings Jelger ___ 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] Re: how to show dodecahedron box in VMD
Thanks lot. Happy Thanksgiving!. -Xianghong Qi On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni < [EMAIL PROTECTED]> wrote: > Tsjerk Wassenaar ha scritto: > >> Hi, >> >> Can't help you with VMD, but I do have a script to take care of this in >> Pymol. >> >> Cheers, >> >> Tsjerk >> >> On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: >> >> >>> Dear all: >>> >>> I am trying to show the dodecahedron box only in vmd since my simulation >>> box >>> is dodecahedron. If I include water, I can see the box is dodecahedron. >>> But >>> I want to get rid off all of water, then my box will not appear there. >>> How >>> can I keep the dodecahedron box boundaries and solute only? Looks like >>> only >>> the rectangular box boundaries can be drawn in VMD. >>> Does anyone has some suggestions? Appreciate your great help. >>> Happy Thanksgiving. >>> -Xianghong Qi >>> >>> -- >>> Some people make the world more special just by being in it. >>> >>> ___ >>> 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 >>> >>> >>> >> >> >> >> > Hi, > you can try this: > > trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact* > > or > > trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1 > > well...the first converts all your trajectory and the last command extracts > 1 frame in a gro file.. > > good luck > alessandro > > > > ___ > 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 > -- Some people make the world more special just by being in it. ___ 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] List of all bonds form tpr file?
Dear All, We have a script, which visualizes the bonds in the coarse-grained system simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files and extracted BONDS records. Now in 4.x it does not work because gmxdump no longer outputs all bonds in the system. Is it possible to extract information about *all* bonds in the system (not only the bonds in each moleculetype) from tpr file in 4.x? Any help is appreciated! Semen - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, November 19, 2008 1:57:19 PM Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation? Semen Esilevsky wrote: > Dear All, > Where can I find documentation about the pull code in Gromacs 4.0? As far as > I understand old style of setting up pulling simulations in separate file > does not work any more, but I can't figure out how to transfer pulling params > correctly to mdp file. Any help is appreciated! > > P.S. Probably the developers could put at least some very brief docs on web > site while new manual is being prepared? Otherwise new cool features of 4.0 > just can't be used by ordinary users... The beta manual is at ftp://ftp.gromacs.org/pub/beta/ 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] Re: Loss of bonds in HEME iron after pdb2gmx
[EMAIL PROTECTED] wrote: Hi Justin, Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said the topology file does contain the bonds and I need not have made the modificatins to specbond.dat. But using the original specbond.dat does not prevent the protonation of CYS. I renamed CYS as CYS2 in the input pdb file and used the following command line pdb2gmx_mpi -ignh -ff gmx -f 2c9_s50.pdb -o protein_h.pdb -p topology.top -water spce Am I missing some crucial option here (like -ss for disulphide bonds)? Thanks once again. One piece of general advice - don't use ffgmx. It has long been deprecated (according to the manual, the output of pdb2gmx, and dozens of posts on this list). Use one of the newer Gromos96 force fields. Now, to address the actual question :) The only thing I can think of is that specbond.dat uses a simple distance search to determine if the atoms are bonded, and I believe the tolerance is something like 10%. So the value in specbond.dat of 0.25 implies that pdb2gmx should expect the S and Fe atoms to be 0.25 +/- 0.2 nm apart. If they are much further apart, no bond will be detected. Check your input .pdb file to see how far apart these two atoms are. -Justin Regards, Sarada Message: 6 Date: Tue, 25 Nov 2008 07:17:14 -0500 From: "Justin A. Lemkul" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=UTF-8; format=flowed [EMAIL PROTECTED] wrote: Hello, Sorry, I realised the HEME HEC naming was not the problem. But still the pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets protonated and doesnot form a bond with HEME. I tried to preserve the bonds by editing the specbond.dat file. I do not know if it can be used for intramolecular bonding. Kindly inform if the modifications I have made are valid. The runtime information during the execution of pdb2gmx indicated the linking of FE in HEME to the N atoms. However, I do not see the bonds when I open the output file in Pymol. Please indicate how this problem can be resolved. Well, using visualization software may not indicate anything. Most programs decide on bonds based on distance, not any sort of intelligent mechanism. The question is whether or not these bonds show up in your topol.top. This is the content of my specbond.dat file: 5 CYS SG 1 HEMEFE 5 0.25CYS HEME Well, this may be why your Cys is getting protonated - you're telling pdb2gmx that it should be! See the format of specbond.dat here: http://wiki.gromacs.org/index.php/specbond.dat The second-to-last column should be the new residue name for cysteine, probably you want something like CYS2. HEMEFE 5 HEMENA 3 0.22HEMEHEME HEMEFE 5 HEMENB 3 0.22HEMEHEME HEMEFE 5 HEMENC 3 0.22HEMEHEME HEMEFE 5 HEMEND 3 0.22HEMEHEME Why is this section (above) even necessary? Are these bonds not defined in the .rtp file of your force field? Which force field are you using? I know these are defined in the Gromos-type force fields. Try again with the original specbond.dat, but don't assume that visualization software will always indicate the presence/absence of a bond. Examine your topology for that. -Justin And these I obtained during the execution of pdbgmx: Opening library file specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Special Atom Distance matrix: CYS122 CYS135 CYS143 CYS146 CYS150 CYS237 CYS309 SG958 SG1059 SG1118 SG1136 SG1165 SG1902 SG2475 CYS135 SG1059 1.677 CYS143 SG1118 1.076 1.092 CYS146 SG1136 1.313 1.792 0.749 CYS150 SG1165 1.175 2.054 0.978 0.426 CYS237 SG1902 2.194 3.510 2.536 1.933 1.632 CYS309 SG2475 1.745 2.703 2.469 2.507 2.423 2.449 CYS343 SG2748 4.679 4.998 4.364 3.763 3.870 3.329 4.426 CYS406 SG3265 2.258 2.657 2.051 1.603 1.744 1.886 2.198 CYS457 SG3657 2.232 0.829 1.894 2.582 2.825 4.173 2.898 HEME462 FE3693 2.257 2.566 1.949 1.489 1.669 1.956 2.343 HEME462 NA3694 2.456 2.680 2.110 1.663 1.862 2.118 2.486 HEME462 NB3695 2.199 2.426 1.883 1.498 1.704 2.088 2.247 HEME462 NC3696 2.061 2.462 1.795 1.321 1.479 1.809 2.217 HEME462 ND3697 2.331 2.711 2.031 1.505 1.657 1.841 2.455 CYS343 CYS406 CYS457 HEME462 HEME462 HEME462 HEME462 SG2748 SG3265 SG3657 FE3693 NA3694 NB3695 NC3696 CYS406 SG3265 2.501 CYS457 SG3657 5.547 3.210 HEME462 FE3693 2.512 0.219 3.147 HEME462 NA3694 2.361 0.325 3.240 0.211 HEME462 NB3695 2.647 0.293
RE: [gmx-users] Using double precision files with single precision version
Hi, This works fine. All Gromacs file format/programs are single/double compatible both ways. Reading a double precision file with a single precision program, or course, gives single precision results. But there is probably no property that is significantly affected by this. Berk > Date: Wed, 26 Nov 2008 20:14:28 +1100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Using double precision files with single precision > version > > vivek sharma wrote: > > Hi All, > > I had a few MD runs with double precision in gromacs, Can I use single > > precision version of gromacs to play with those files e.g making movie > > files and extracting h_bond information. > > I am afraid if it will affect my results. > > I don't know whether it does work, but I suspect not. However it's > trivial to compile a double-precision version, with --enable-double and > --program-suffix=_d, and once installed you can use g_hbond when you > want and g_hbond_d when you want. > > 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Bugs in gromacs 4
Jelger Risselada wrote: > Finally had a look through the gromacs 4.0 source code. > Don't know if this bug/points already have been reported and changed in > 4.0.2: > > 1) There is never memory allocated for the pointers to the user defined > groups: > > mdatoms->cU1 etc. I'm not sure, but there is a /* The user should fix this */ if (FALSE) srenew(md->cU1,md->nalloc); if (FALSE) srenew(md->cU2,md->nalloc); in ./src/mdlib/mdatom.c. You can remove the FALSE and get the memory allocation, I guess. Jochen > > These pointers will stay NULL when a user defined group is defined in > the mdp file. > I find these groups normally a pretty useful interface for simple fast > implementations. > > 2) The pull code has indeed completely changed, however to me the > questionable factor 0.5 remained the same: > In pull.c: > > /* Add the pull contribution to the virial */ > vir[j][m] += 0.5*f[j]*r_ij[g][m]; > > I do agree with the positive sign of the summation, but why is there a > factor 0.5 to correct for double counting included in the summation. The > summation is already ordered as r_ij and f[j] is the distance vector and > force between the particle and the equilibrium position of the spring > and therefore double counting cannot occur. Ofcourse it's possible that > this factor 0.5 is not meant as a double counting correction factor, but > then I don't see where it does come from. If this factor is indeed > incorrect it might affect the pressure significantly in case a large > pulling group is used. > > greetings > > Jelger > > > > > > > > > > > > > > > > > > > > > > > > > > ___ > 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 > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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] Bugs in gromacs 4
Jochen Hub wrote: Jelger Risselada wrote: Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms->cU1 etc. I'm not sure, but there is a /* The user should fix this */ if (FALSE) srenew(md->cU1,md->nalloc); if (FALSE) srenew(md->cU2,md->nalloc); in ./src/mdlib/mdatom.c. You can remove the FALSE and get the memory allocation, I guess. Jochen A hardcoded if(FALSE) in the middle of no where with the command /*The user should fix this */ . How flexible.. ;-) greetings Jelger These pointers will stay NULL when a user defined group is defined in the mdp file. I find these groups normally a pretty useful interface for simple fast implementations. 2) The pull code has indeed completely changed, however to me the questionable factor 0.5 remained the same: In pull.c: /* Add the pull contribution to the virial */ vir[j][m] += 0.5*f[j]*r_ij[g][m]; I do agree with the positive sign of the summation, but why is there a factor 0.5 to correct for double counting included in the summation. The summation is already ordered as r_ij and f[j] is the distance vector and force between the particle and the equilibrium position of the spring and therefore double counting cannot occur. Ofcourse it's possible that this factor 0.5 is not meant as a double counting correction factor, but then I don't see where it does come from. If this factor is indeed incorrect it might affect the pressure significantly in case a large pulling group is used. greetings Jelger ___ 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] Problems with distance restraints
It's not really a solution, but you could try a different number of nodes. I have found that even regular topologies might run on N nodes, but not N+A nodes, giving the error messaeg that you post below. Chris. -- original message -- Hi all, I am trying to use a simple scheme to restrain a few distances within my protein, which is contained within an octahedral box of SPC water. In place of distance restraints, I'm using bond type 6 to utilize a harmonic potential to restrain the distance between a few atoms. When I imposed one such restraint in the topology, the simulation ran fine. After finishing this trajectory, I wanted to impose a second restraint and try again. At this point, the simulation fails with the following: mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt Initializing Domain Decomposition on 24 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 1.634 nm multi-body bonded interactions: 0.606 nm Minimum cell size due to bonded interactions: 1.797 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm Estimated maximum distance required for P-LINCS: 0.876 nm Guess for relative PME load: 0.45 Will use 12 particle-particle and 12 PME only nodes This is a guess, check the performance at the end of the log file Using 12 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm The maximum allowed number of cells is: X 2 Y 2 Z 2 --- Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2 Source code file: domdec.c, line: 5842 Fatal error: There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 2.24633 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- "I'm Only Faking When I Get It Right" (Soundgarden) I realize there are more optimizations I could impose to better balance the PP/PME load. I have tried those (altering my cutoff's and grid spacing) but it makes no difference. Plus, I'd like to remain consistent with the original simulation that used only one restraint. If I remove the second restraint, the simulation runs just fine. For reference, the restraints I'm imposing are: 330 1016 60.669 5.0300e+06 1016 559 60.376 5.0300e+06 The box vectors from the .gro file are: 7.14132 6.73290 5.83086 0.0 0.0 2.38044 0.0 -2.38044 3.36645 Is there anything obvious that I'm doing wrong? Or should I just use real distance restraints, according to manual section 4.3.4? Thanks for any insights. -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
RE: [gmx-users] course grain model for DNA
Hi Justin, Thank you for your reply. In fact , for this base pair of "Gb2 Cb2 1 0.000194e10 0.00217e4", whatever I do , the final result for this base pair is the same they will always separate from each other. Hence, I doubt whether this is because gromacs did not read my force field file at all. I hope to get your further suggestions about that. Thank you . Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 25, 2008 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] course grain model for DNA He, Yang wrote: > Hi all users, > > when I am using the gromacs to simulate the course grain model for DNA, it > seems that the software doesn't recognize my force field file. I have > included all the bond and non-bond parameters in the bon.itp and nb.itp file. > > During my simulation , I found that the base pair for C-G which first are in > the balance distance always repel from each other so I try to increase the > value of epsilon to increase the dispersion between this pair but it still > did not work and the pair still repelled from each other after the > simulation . > > Then I tried like this " ; Gb2 Cb2 1 0.000194e10 0.00217e4 " > in my nb.itp file, I found that the simulation can still be carried on and > the simulation result is the same for this base pair. > Well, that line is commented out (;), so naturally it would have no effect. -Justin > So ,I got confused about this phenomenon . Can anyone of you give me some > suggestions? > > Thank you in advance. > > Yang > ___ > 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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [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] course grain model for DNA
Hi Mrinalini. Thank you for your suggestions. In my previous case, I never use the distance restraints . So I wonder whether you can provide me a sample for file of the disres.itp .In fact, I don't know much about this file' form and how to set values in the file. Thank you. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mrinalini Puranik [EMAIL PROTECTED] Sent: Tuesday, November 25, 2008 3:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] course grain model for DNA If there is fraying at the edges only, you can impose distance restraints on some of the hydrogen bonds at the ends. You need to modify md.mdp to turn on distance restraints and have a new file called disres.itp that mentions the distances to be restrained. Hope this helps, Mrinalini On Wed, Nov 26, 2008 at 1:06 AM, He, Yang <[EMAIL PROTECTED]> wrote: > Hi all users, > > when I am using the gromacs to simulate the course grain model for DNA, it > seems that the software doesn't recognize my force field file. I have > included all the bond and non-bond parameters in the bon.itp and nb.itp file. > > During my simulation , I found that the base pair for C-G which first are in > the balance distance always repel from each other so I try to increase the > value of epsilon to increase the dispersion between this pair but it still > did not work and the pair still repelled from each other after the > simulation . > > Then I tried like this " ; Gb2 Cb2 1 0.000194e10 0.00217e4 " > in my nb.itp file, I found that the simulation can still be carried on and > the simulation result is the same for this base pair. > > So ,I got confused about this phenomenon . Can anyone of you give me some > suggestions? > > Thank you in advance. > > Yang > ___ > 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 > -- Mrinalini Puranik ___ 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] course grain model for DNA
He, Yang wrote: Hi Mrinalini. Thank you for your suggestions. In my previous case, I never use the distance restraints . So I wonder whether you can provide me a sample for file of the disres.itp .In fact, I don't know much about this file' form and how to set values in the file. Manual section 4.3.4; it doesn't have to be a separate .itp file if you don't want. You can just add a [ distance_restraints ] section in your system topology. -Justin Thank you. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mrinalini Puranik [EMAIL PROTECTED] Sent: Tuesday, November 25, 2008 3:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] course grain model for DNA If there is fraying at the edges only, you can impose distance restraints on some of the hydrogen bonds at the ends. You need to modify md.mdp to turn on distance restraints and have a new file called disres.itp that mentions the distances to be restrained. Hope this helps, Mrinalini On Wed, Nov 26, 2008 at 1:06 AM, He, Yang <[EMAIL PROTECTED]> wrote: Hi all users, when I am using the gromacs to simulate the course grain model for DNA, it seems that the software doesn't recognize my force field file. I have included all the bond and non-bond parameters in the bon.itp and nb.itp file. During my simulation , I found that the base pair for C-G which first are in the balance distance always repel from each other so I try to increase the value of epsilon to increase the dispersion between this pair but it still did not work and the pair still repelled from each other after the simulation . Then I tried like this " ; Gb2 Cb2 1 0.000194e10 0.00217e4 " in my nb.itp file, I found that the simulation can still be carried on and the simulation result is the same for this base pair. So ,I got confused about this phenomenon . Can anyone of you give me some suggestions? Thank you in advance. Yang ___ 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 -- Mrinalini Puranik ___ 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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] course grain model for DNA
He, Yang wrote: Hi Justin, Thank you for your reply. In fact , for this base pair of "Gb2 Cb2 1 0.000194e10 0.00217e4", whatever I do , the final result for this base pair is the same they will always separate from each other. Hence, I doubt whether this is because gromacs did not read my force field file at all. I hope to get your further suggestions about that. What magnitude of values have you tried? Using 0.000194e10 (1.94e7) for epsilon seems huge, but then, the only CG force field I've ever used is MARTINI (and only with only a little experience). The magnitudes of sigma and epsilon for that force field are on the order of e0, e-01, etc. How are you determining your sigma and epsilon values? -Justin Thank you . Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 25, 2008 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] course grain model for DNA He, Yang wrote: Hi all users, when I am using the gromacs to simulate the course grain model for DNA, it seems that the software doesn't recognize my force field file. I have included all the bond and non-bond parameters in the bon.itp and nb.itp file. During my simulation , I found that the base pair for C-G which first are in the balance distance always repel from each other so I try to increase the value of epsilon to increase the dispersion between this pair but it still did not work and the pair still repelled from each other after the simulation . Then I tried like this " ; Gb2 Cb2 1 0.000194e10 0.00217e4 " in my nb.itp file, I found that the simulation can still be carried on and the simulation result is the same for this base pair. Well, that line is commented out (;), so naturally it would have no effect. -Justin So ,I got confused about this phenomenon . Can anyone of you give me some suggestions? Thank you in advance. Yang ___ 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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genbox -ci solute.gro -nmol N
Hi Originally, in the topol.top file => [molecule] solute 1 After the command: genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N -p topol.top in the topol.top file => [molecule] solute 1 solvent 5000 I think the flag "-p topol.top" in the genbox command did not do it correctly. I am considering the two possible modification on the topol.top file [molecule] solute (1+N) solvent 5000 [molecule] solute (1+N) solvent (5000 - N) Which one is correct? Or, none of them is correct? What is the correct form of it? Thank you Lin ___ 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] genbox -ci solute.gro -nmol N
Chih-Ying Lin wrote: Hi Originally, in the topol.top file => [molecule] solute 1 After the command: genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N -p topol.top in the topol.top file => [molecule] solute 1 solvent 5000 I think the flag "-p topol.top" in the genbox command did not do it correctly. I am considering the two possible modification on the topol.top file [molecule] solute (1+N) solvent 5000 [molecule] solute (1+N) solvent (5000 - N) Which one is correct? Depends, what's in the genbox output structure? Or, none of them is correct? What is the correct form of it? It is often easier to insert a molecule with -ci, then solvate in the next step (at least from a conceptual standpoint). I don't know how the code will handle it, but it should certainly clear up your confusion. -Justin Thank you Lin ___ 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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Concentration
Hi How to make a solution with specific concentration ? Command 1 => editconf -d 0.75 -bt cubic 0.75=Distance between the solute and the box cubic = the type of the simulation box Command 2 => genbox -cp solute.gro -cs spc.gro -box Y Y Y Y = the box vector in nm If I use cubic in my system, is Y defined as the length of the cubic in the three directions? Is the overall volume of the simulation box = Y * Y *Y (nm*nm*nm) ? Is the center of cubic on the origin (0,0,0) of the coordinate? Thank you Lin ___ 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] Concentration
Chih-Ying Lin wrote: Hi How to make a solution with specific concentration ? Concentration of what? For ions, use genion -conc; for other solute molecules, do some simple stoichiometry from General Chemistry based on the box volume. Command 1 => editconf -d 0.75 -bt cubic 0.75=Distance between the solute and the box cubic = the type of the simulation box Command 2 => genbox -cp solute.gro -cs spc.gro -box Y Y Y Y = the box vector in nm If I use cubic in my system, is Y defined as the length of the cubic in the three directions? Yes, that's what you've instructed genbox to do. Is the overall volume of the simulation box = Y * Y *Y (nm*nm*nm) ? Yes. Is the center of cubic on the origin (0,0,0) of the coordinate? No. By convention, the system will be centered at (Y/2) in each direction. If you're setting up your system using the above commands, it might be easier to just combine the box creation into one step with editconf (which will also print the coordinates of the system center): editconf -bt cubic -box Y -c -Justin Thank you Lin ___ 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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problems running grompp with protein-ligand complex
I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of molecules all match, the ligand coordinates are still there but grompp tells me that: Fatal error: Found a second defaults directive, file "ligand.itp", line 5 I've checked wikigromacs, but the solution given there, to simply erase the second default line does not suit me here. Once I do this, i mean, go to my ligand.itp file and put a ; before my default section, grompp does not recognize anymore that my ligand is there and gives out another error line. I would like some advice on the matter if possible. Thank you in advance Fabrício Bracht ___ 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] problems running grompp with protein-ligand complex
Can you post the contents of your ligand.itp? -Justin Ragnarok sdf wrote: I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of molecules all match, the ligand coordinates are still there but grompp tells me that: Fatal error: Found a second defaults directive, file "ligand.itp", line 5 I've checked wikigromacs, but the solution given there, to simply erase the second default line does not suit me here. Once I do this, i mean, go to my ligand.itp file and put a ; before my default section, grompp does not recognize anymore that my ligand is there and gives out another error line. I would like some advice on the matter if possible. Thank you in advance Fabrício Bracht ___ 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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] no density option in g_energy
Dear all, Why there is no density option when I do g_energy amalyzation. thanks QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. ___ 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] no density option in g_energy
Q. Y. HUAN wrote: Dear all, Why there is no density option when I do g_energy amalyzation. This question was asked just a few weeks ago (hint: search the list for answers!). Searching "no density g_energy" will lead you to this: http://www.gromacs.org/pipermail/gmx-users/2008-November/037712.html -Justin thanks QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. ___ 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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] SMP/Parallel mdrun
I am a computational scientist working with a physical chemist to try to parallelize her use of gromacs -- today is my first day using the application and I am not succeeding in getting multiple threads. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 however there is then only a single thread executing. Do I need to preprocess the topology file? In the first instance, getting mdrun going in parallel on an SMP machine is the higher priority. Next I will look at running it on a cluster. TIA. Ian -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org ___ 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] SMP/Parallel mdrun
Ian Stokes-Rees wrote: I am a computational scientist working with a physical chemist to try to parallelize her use of gromacs -- today is my first day using the application and I am not succeeding in getting multiple threads. Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 -N does nothing, and -np is no longer accepted - as you'd know from reading mdrun -h, right? Like most MPI parallel codes, you need to use mpirun. If your lam environment is correctly configured, then I think you will not need -np 4 as an argument to mpirun. Also, probably you are actually running a non-MPI gromacs, since by default, using --enable-mpi will suffix mdrun to be mdrun_mpi. however there is then only a single thread executing. Do I need to preprocess the topology file? Not with gromacs 4. 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] SMP/Parallel mdrun
Hi Mark, Mark Abraham wrote: Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. Yes, I gathered that. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 -N does nothing, and -np is no longer accepted - as you'd know from reading mdrun -h, right? That is a bit of a condecending way of putting it. If I knew -N did nothing and -np was no longer accepted, then of course I would not have used them. In fact, I was reading the documentation from a file called "manual-4.0.pdf" which stated: " If you have a single machine with multiple processors you don’t have to use the mpirun com- mand, but you can do with an extra option to mdrun: % mdrun -np 8 -s topol -v -N 8 " so that is where I took the example from. I think this PDF was linked from the gromacs "documentation" section of the website. Like most MPI parallel codes, you need to use mpirun. If your lam environment is correctly configured, then I think you will not need -np 4 as an argument to mpirun. Also, probably you are actually running a non-MPI gromacs, since by default, using --enable-mpi will suffix mdrun to be mdrun_mpi. Doesn't look like it: $ ./configure --prefix=/opt/osg-shared/se/app/site --with-pic --enable-mpi $ make $ make install $ ls /opt/osg-shared/se/app/site/bin/ | grep mdrun mdrun Anyway, thanks for your suggestions because I now have it working via: $ mpirun -np 4 /opt/osg-shared/se/app/site/bin/mdrun -s ../1WOM.tpr -v -N 4 and I see 4 processes running at 100% and an estimated run time 25% of the serial version. Ian. -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org ___ 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] SMP/Parallel mdrun
Ian Stokes-Rees wrote: Hi Mark, Mark Abraham wrote: Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. Yes, I gathered that. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 -N does nothing, and -np is no longer accepted - as you'd know from reading mdrun -h, right? That is a bit of a condecending way of putting it. If I knew -N did nothing and -np was no longer accepted, then of course I would not have used them. In fact, I was reading the documentation from a file called "manual-4.0.pdf" which stated: " If you have a single machine with multiple processors you don’t have to use the mpirun com- mand, but you can do with an extra option to mdrun: % mdrun -np 8 -s topol -v -N 8 " so that is where I took the example from. I think this PDF was linked from the gromacs "documentation" section of the website. Hmmm that's been in the documentation since v3.3 and I've never seen code that might make it work. That looks like a documentation error. 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] Re: About entropic contribution to the potential of mean force
I've got it! Thanks myself. ^_^ So, it seems that the prior calculations by, i.e. Ciccotti, et al, Chem. Phys. 129, 241 (1989), Guardia, et al, J. Chem. Phys. 95, 2823 (1991) are flawy since they have not corrected the entropic effects at all. Cheers, zgzhang > Date: Wed, 26 Nov 2008 15:55:05 +0800 > From: "Zhang Zhigang" <[EMAIL PROTECTED]> > Subject: [gmx-users] About entropic contribution to the potential of >meanforce > To: gmx-users@gromacs.org > Message-ID: ><[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, >In the manual of gromacs, the entropic contribution to the pmf is > emphasized. In my opinion, this contribution is originated from the > rotations of the constrained groups. >However, according to the manual suggestion, "...when calculating a PMF > between two solutes in a solvent, for the purpose of simulating without > solvent, the entropic contribution should be removed." I'm really confused > with this. >If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl- > and many water molecules), I want to calculate the potential of mean force > of NaCl, should I count the contributions from the entropic effects? >According to Hess et al., (2006), JCP, 124: 164509, this effect should > surely be added. >So, any one experienced with similar researches can give me an answer > for this: when should I add the entropic contribution to the pmfs? and, > what > the really physical explanation for this effect? >Thanks in advance! > > Regards, > > zgzhang > ___ 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] Re: Re: Loss of bonds in HEME iron after pdb2gmx
Hi Justin, Thanks a lot for the suggestions regarding the force field and the sulphide bond. The bond is now formed after changing the distance range in specbond.dat. Thanks. Sarada > > Message: 2 > Date: Wed, 26 Nov 2008 07:21:37 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > [EMAIL PROTECTED] wrote: >> Hi Justin, >> Thanks for your reply. I am using the gmx Gromacs Forcefield. As you >> said >> the topology file does contain the bonds and I need not have made the >> modificatins to specbond.dat. But using the original specbond.dat does >> not >> prevent the protonation of CYS. I renamed CYS as CYS2 in the input pdb >> file and used the following command line >> pdb2gmx_mpi -ignh -ff gmx -f 2c9_s50.pdb -o protein_h.pdb -p >> topology.top -water spce >> Am I missing some crucial option here (like -ss for disulphide bonds)? >> Thanks once again. > > One piece of general advice - don't use ffgmx. It has long been > deprecated > (according to the manual, the output of pdb2gmx, and dozens of posts on > this > list). Use one of the newer Gromos96 force fields. > > Now, to address the actual question :) The only thing I can think of is > that > specbond.dat uses a simple distance search to determine if the atoms are > bonded, > and I believe the tolerance is something like 10%. So the value in > specbond.dat > of 0.25 implies that pdb2gmx should expect the S and Fe atoms to be 0.25 > +/- 0.2 > nm apart. If they are much further apart, no bond will be detected. > Check your > input .pdb file to see how far apart these two atoms are. > > -Justin > >> Regards, >> Sarada >> >> >>> Message: 6 >>> Date: Tue, 25 Nov 2008 07:17:14 -0500 >>> From: "Justin A. Lemkul" <[EMAIL PROTECTED]> >>> Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx >>> To: Discussion list for GROMACS users >>> Message-ID: <[EMAIL PROTECTED]> >>> Content-Type: text/plain; charset=UTF-8; format=flowed >>> >>> >>> >>> [EMAIL PROTECTED] wrote: Hello, Sorry, I realised the HEME HEC naming was not the problem. But still the pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets protonated and doesnot form a bond with HEME. I tried to preserve the bonds by editing the specbond.dat file. I do not know if it can be used for intramolecular bonding. Kindly inform if the modifications I have made are valid. The runtime information during the execution of pdb2gmx indicated the linking of FE in HEME to the N atoms. However, I do not see the bonds when I open the output file in Pymol. Please indicate how this problem can be resolved. >>> Well, using visualization software may not indicate anything. Most >>> programs >>> decide on bonds based on distance, not any sort of intelligent >>> mechanism. >>> The >>> question is whether or not these bonds show up in your topol.top. >>> This is the content of my specbond.dat file: 5 CYS SG 1 HEMEFE 5 0.25CYS HEME >>> Well, this may be why your Cys is getting protonated - you're telling >>> pdb2gmx >>> that it should be! See the format of specbond.dat here: >>> >>> http://wiki.gromacs.org/index.php/specbond.dat >>> >>> The second-to-last column should be the new residue name for cysteine, >>> probably >>> you want something like CYS2. >>> HEMEFE 5 HEMENA 3 0.22HEMEHEME HEMEFE 5 HEMENB 3 0.22HEMEHEME HEMEFE 5 HEMENC 3 0.22HEMEHEME HEMEFE 5 HEMEND 3 0.22HEMEHEME >>> Why is this section (above) even necessary? Are these bonds not >>> defined >>> in the >>> .rtp file of your force field? Which force field are you using? I >>> know >>> these >>> are defined in the Gromos-type force fields. >>> >>> Try again with the original specbond.dat, but don't assume that >>> visualization >>> software will always indicate the presence/absence of a bond. Examine >>> your >>> topology for that. >>> >>> -Justin >>> And these I obtained during the execution of pdbgmx: Opening library file specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Special Atom Distance matrix: CYS122 CYS135 CYS143 CYS146 CYS150 CYS237 CYS309 SG958 SG1059 SG1118 SG1136 SG1165 SG1902 SG2475 CYS135 SG1059 1.677 CYS143 SG1118 1.076 1.092 CYS146 SG1136 1.313 1.792 0.749 CYS150 SG1165 1.175 2.054 0.978 0.426 CYS237 SG1902 2.194 3.510 2.536 1.933 1.632 CYS309 SG2475 1.745 2.703 2.469 2.507 2.423 2.449 >>>
Re: [gmx-users] no density option in g_energy
Dear Justin, Thankk you very much for yr reply. I have forgotten that my system is under NVT condition. Thanks. QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. --- On Thu, 11/27/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] no density option in g_energy > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > > Date: Thursday, November 27, 2008, 9:22 AM > Q. Y. HUAN wrote: > > Dear all, Why there is no density option when I do > g_energy amalyzation. > > > > This question was asked just a few weeks ago (hint: search > the list for answers!). Searching "no density > g_energy" will lead you to this: > > http://www.gromacs.org/pipermail/gmx-users/2008-November/037712.html > > -Justin > > > thanks > > > > QIU YI HUAN > > DEPARTMENT OF CHEMISTRY, > > FACULTY OF SCIENCE, > > UNIVERSITY PUTRA MALAYSIA, > > MALAYSIA. > > > > > > ___ > > 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 > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems running grompp with protein-ligand complex
Hi Fabrício, > I've checked wikigromacs, but the solution given there, to simply erase the > second default line does not suit me here. Once I do this, i mean, go to my > ligand.itp file and put a ; before my default section, grompp does not > recognize anymore that my ligand is there and gives out another error line. Well, it's not like grompp is recognizing you have a ligand there right now, is it? grompp doesn't reach the point where it realizes you don't seem to have a ligand. It seems there's something wrong with the topology. Better post ligand.itp, like Justin suggests, and also give the error which occurs when you do comment out the defaults line in the ligand topology. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php