Here are the details of my .mdp file, I use PME, cutoff 1.0 nm, and time step 2 fs......
dt = 0.002 ; time step (ps) nsteps = 100000 ; number of steps comm_mode = Linear comm_grps = System energygrps = OW HW nstcomm = 10 ; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 500 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw = 1.0 ; cut-off for vdw rcoulomb = 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t = 0.5 ref_t = 300 Thanks -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, June 07, 2006 3:35 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 26, Issue 32 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Free volume: Pass and Gromacs (Alessandro Mattozzi) 2. Re: Free volume: Pass and Gromacs (David van der Spoel) 3. Re: Freezing part of the molecules!!! (Soren Enemark) 4. Re: Freezing part of the molecules!!! (David van der Spoel) 5. shake vs settle for water (Rahul Godawat) 6. diffusivity computations (Debashis Dutta) 7. Re: shake vs settle for water (David van der Spoel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 7 Jun 2006 17:11:03 +0200 From: "Alessandro Mattozzi" <[EMAIL PROTECTED]> Subject: [gmx-users] Free volume: Pass and Gromacs To: <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? -Segmentation fault Suggestion: I use trjconv to get a pdb; is it possible that I am doing some mistake in the conversion? Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060607/ace7fa15/att achment-0001.html ------------------------------ Message: 2 Date: Wed, 07 Jun 2006 17:14:59 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Free volume: Pass and Gromacs To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Alessandro Mattozzi wrote: > Hi all > I wonder if anybody has been using Pass to measure free volume: I got > these errors: > > -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. > Suggestion: Do I have to remove all the dummies? Yes. make an index file, it will have a suitable group for it. > > -Segmentation fault > Suggestion: I use trjconv to get a pdb; is it possible that I am doing > some mistake in the conversion? > > Thanx > > Alessandro Mattozzi > M.Phil., Ph.D. student > Dept. of Fibre and Polymer Technology > Royal Institute of Technology > Stockholm, Sweden > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-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 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------ Message: 3 Date: Wed, 7 Jun 2006 18:32:42 +0200 From: Soren Enemark <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Freezing part of the molecules!!! To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ] 106 107 ... [ Group3 ] .... where atoms number 45, 46, 47, 48, and 49 etc belong to your 1st group and so on. Remember to use the numbering as it is in the gro file. This you can do with "make_ndx -f your_gro_file.gro" 2. Add the folling to your mdp file: freezegrps = Group1 Group2 Group3 Group4 Group5 freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Note that for each group defined as freezegroup you need to specify the dimensions that you want to freeze (x y z). This is done with either Y or N. So if you want only to freeze Group1 in the z-direction you write: freezegrps = Group1 freezedim = N N Y All the best, Soren Quoting Marcelo Fabricio Masman <[EMAIL PROTECTED]>: > Hi all!!! > > I am trying to run a MD simulation with part of my system frozen. I was > looking into the manual but I couldn't find the answer since the manual says > the way for freezing complete groups. I would like to freeze only a part of > my protein and permit the completed optimization of the rest. For example, > my protein group has 5 protein chains with 42 residues each of them. I would > like to freeze (in all directions) the alfa Carbon atoms for residues 18-42 > for each chain. Does somebody know if it is possible to do such thing with > GROMACS? Can somebody help me? > > Thanks a lot, in advance > > Marcelo > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ ------------------------------ Message: 4 Date: Wed, 07 Jun 2006 19:27:50 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Freezing part of the molecules!!! To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Soren Enemark wrote: > Hi Marcelo, > what you need to do is: > > 1. create an index file (.ndx) with the groups that you want to freeze. > Such an index file should look like: > [ Group1 ] > 45 46 47 48 49 ... > [ Group2 ] > 106 107 ... > [ Group3 ] > .... > > where atoms number 45, 46, 47, 48, and 49 etc belong to your 1st group and > so on. Remember to use the numbering as it is in the gro file. > This you can do with "make_ndx -f your_gro_file.gro" > > 2. Add the folling to your mdp file: > freezegrps = Group1 Group2 Group3 Group4 Group5 > freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y > > Note that for each group defined as freezegroup you need to specify the > dimensions that you want to freeze (x y z). This is done with either > Y or N. So if you want only to freeze Group1 in the z-direction you write: > freezegrps = Group1 > freezedim = N N Y > > All the best, > Soren > Just as a warning: please note that combining: constraints + freeze groups + pressure coupling will give undefined results. > Quoting Marcelo Fabricio Masman <[EMAIL PROTECTED]>: > > >>Hi all!!! >> >>I am trying to run a MD simulation with part of my system frozen. I was >>looking into the manual but I couldn't find the answer since the manual says >>the way for freezing complete groups. I would like to freeze only a part of >>my protein and permit the completed optimization of the rest. For example, >>my protein group has 5 protein chains with 42 residues each of them. I would >>like to freeze (in all directions) the alfa Carbon atoms for residues 18-42 >>for each chain. Does somebody know if it is possible to do such thing with >>GROMACS? Can somebody help me? >> >>Thanks a lot, in advance >> >>Marcelo >> > > > > > > ------------------------------------------------- > This mail sent through IMP: http://horde.org/imp/ > > _______________________________________________ > gmx-users mailing list gmx-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 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------ Message: 5 Date: Wed, 7 Jun 2006 13:15:24 -0400 From: "Rahul Godawat" <[EMAIL PROTECTED]> Subject: [gmx-users] shake vs settle for water To: <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" Hi All, I am using Groamcs 3.2.1 for my simulations, I am having some problems with an interfacial system when I use SETTLE as opposed to SHAKE to constrain OH bonds and HOH angle in water. As a matter of fact I did various simulations of liquid vapor interface simulations of water, SETTLE gives me absurd numbers while SHAKE gives consistently good results . I have looked up the mailing list as well as manual for differences in SHAKE and SETTLE, but apart from the statement that SETTLE Is better than SHAKE I dint find much. Any ideas on how to resolve this. When I look at OH bond and HOH angle distribution from SETTLE and SHAKE it's precisely same. Any insights would be helpful, Thanks Rahul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060607/3f8308b8/att achment-0001.html ------------------------------ Message: 6 Date: Wed, 07 Jun 2006 15:02:28 -0400 From: Debashis Dutta <[EMAIL PROTECTED]> Subject: [gmx-users] diffusivity computations To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII; format="flowed" Hi, I have trying to estimate the diffusivity of an alanine molecule in water with the following .mdp file (for md simualtions). ; Preprocessing title = Alanine with Water cpp = /lib/cpp include = define = ; Run Control integrator = md tinit = 0.000 dt = 0.002 nsteps = 250000 init_step = 0 comm_mode = None nstcomm = 1 comm_grps = ; Langevin Dynamics ; Energy Miimization ; Shell Molecular Dynamics ; Output Control nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstxtcout = 500 xtc_precision = energygrps = System ; Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 ; Electrostatics and VdW coulombtype = PME rcoulomb_switch = 0 rcoulomb = 0.9 vdwtype = shift rvdw_switch = 0 rvdw = 1.4 DispCorr = no table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; Temperature Coupling tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 300 ; Pressure Coupling Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Simulated Annealing ; Velocity Generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ; Bonds constraints = none constraint_algorithm = lincs unconstrained_start = no shake_tol = 0.0001 lincs_order = 4 lincs_iter = 4 lincs_warnangle = 30 morse = no ; Energy Group Exclusions ; NMR Refinement ; Free Energy Perturbation ; Non-equilibrium MD ; Electric Fields ; User Defined Thingies When I plot the mean square displacement, however I do not see a linear variation with time (which is what I expected). Moreover, the estimated diffusivity (using the g_msd command) looks reasonable (1e-5 cm^2/s) for runs shorter than 0.1 ns. If I run it further, the diffusivity keeps increasing to values of 1e-3 cm^2/s (for 10 ns runs). Any comments or sugestions? ___________________________________________________________________________ ------------------------------ Message: 7 Date: Wed, 07 Jun 2006 21:29:03 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] shake vs settle for water To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=windows-1252; format=flowed Rahul Godawat wrote: > Hi All, > > > > I am using Groamcs 3.2.1 for my simulations, I am having some problems > with an interfacial system when I use SETTLE as opposed to SHAKE to > constrain OH bonds and HOH angle in water. As a matter of fact I did > various simulations of liquid vapor interface simulations of water, > SETTLE gives me absurd numbers while SHAKE gives consistently good > results . I have looked up the mailing list as well as manual for > differences in SHAKE and SETTLE, but apart from the statement that > SETTLE Is better than SHAKE I dint find much. Any ideas on how to > resolve this. > > When I look at OH bond and HOH angle distribution from SETTLE and SHAKE > it's precisely same. more details please. time step, cutoffs, PME OS why 3.2.1? > > Any insights would be helpful, > > > > Thanks > > Rahul > > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-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 list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users End of gmx-users Digest, Vol 26, Issue 32 ***************************************** _______________________________________________ gmx-users mailing list gmx-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