Re: [gmx-users] genion problem: is replacing 84 water molecules instead of 200
Subhrangshu Supakar wrote: Hi All !! I have defined my own system which contains 200 water molecules, which I can see in the .gro file. Then I created the .tpr file for 200 steps to steep. In the confout file I can again see the 200 water molecules. But When I am trying to replace the 200 water molecules with 200 Na+ GROMACS is complaining: genion -h is your friend. check the -rmin option. Replacing solvent molecule 144 (atom 4632) with Na Replacing solvent molecule 193 (atom 4779) with Na Replacing solvent molecule 49 (atom 4347) with Na Replacing solvent molecule 84 (atom 4452) with Na --- Program genion, VERSION 3.3.2 Source code file: gmx_genion.c, line: 84 Fatal error: No more replaceable solvent! --- It is replacing 84 water molecules only (I used genion for this) Can any body help me? Thanx in advance. Subhrangshu Supakar ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] Test-set problem with Gromacs 3.3.3
[EMAIL PROTECTED] wrote: Dear gmx-users, I just updated my operating system to Centos 5.1 and Gromacs to version 3.3.3 and faced some problems with test-set (gmxtest-3.3.2.tgz). I can pass all the double precision tests (./gmxtest.pl -double all), but number of single precision tests are failed (./gmxtest.pl all). I looked at the files for these tests, and noticed that the corresponding tests include Coulombic and LJ 1-4 interactions, for which the calculated energies are all zero, whereas the reference energies are non-zero with values even 1000-2000 kJ/mol. Does anyone know reason for such differences? This actually points to possible compilation problems, and hence shows the value of the test set. Please check every step in the compilation process, and also which executable you are running (which mdrun) and which libraries (ldd `which mdrun`). Thanks for your help, Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 +358 50 3474223 E-mail: [EMAIL PROTECTED] [EMAIL PROTECTED] -- ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] atomtypes, parameters in file do not match parameters in manual
Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp file begins with the following lines: [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG Why do the manual parameters not match the parameters in the file? Which of the two are correct? Kind regards Andreas ___ 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] atomtypes, parameters in file do not match parameters in manual
Andreas Kring wrote: Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp file begins with the following lines: [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG Why do the manual parameters not match the parameters in the file? Hm Iäm sure you know the answer to that one. Which of the two are correct? The files. Kind regards Andreas ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] atomtypes, parameters in file do not match parameters in manual
Andreas Kring wrote: Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp file begins with the following lines: [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG Why do the manual parameters not match the parameters in the file? Which of the two are correct? There's an undocumented feature where the fields in an [ atomtypes ] line follow one of several possible formats and grompp is smart about working one which field means what. 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] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen ___ 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] angle analysis
Dear GMX users, I want to analyse th ebond angle. I have used mk_angndx -s md1.tpr -n angle.ndx to prepare an index for g_angle. After g_angle -f md1.xtc -s md1.tpr -n angle.ndx I have obtained Software inconsistency error: Not supported in get_stx_coordnum Most likely this is a trivial question and I did some stupid mistake but I would be thankful for help. Thank you in advance Zuzana ___ 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] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Quoting maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? You'll have to describe how you minimized and equilibrated your bilayer before we'll have any idea what's going on. Also have a thorough look through the archives; many users have posted about bilayers exploding (including yours truly). -Justin Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. And as an aside, broken bonds are only a visualization effect; mdrun doesn't write broken molecules. Also, providing your .mdp file would be of use. -Justin The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? You'll have to describe how you minimized and equilibrated your bilayer before we'll have any idea what's going on. Also have a thorough look through the archives; many users have posted about bilayers exploding (including yours truly). -Justin Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 9
Dear all greeting I am a new user in gromacs . To begin, I need to know how to generate date for simple water molecule and observe vibrational modes. I use this command as well as read in the manual: pdb2gmx -f prot.pdb -o prot.gro -p prot.top but when I choose ff 43a1 Opening library file /usr/share/gromacs/top/ffG43a1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading prot.pdb... I have this error: Program pdb2gmx, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: prot.pdb On Fri, Apr 4, 2008 at 12:00 PM, [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubI ascribe 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. RE: difference between pbc = full and pbc =xy (Berk Hess) 2. Re: genion problem: is replacing 84 water molecules instead of 200 (David van der Spoel) 3. Re: Test-set problem with Gromacs 3.3.3 (David van der Spoel) -- Message: 1 Date: Fri, 4 Apr 2008 03:50:40 +0200 From: Berk Hess [EMAIL PROTECTED] Subject: RE: [gmx-users] difference between pbc = full and pbc =xy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi, All options are described in share/html/online/mdp_opt.html pbc=xy is what you would (probably) guess pbc in x and y only. pbc=full is replaced by periodic_molecules, such that it can also be used with pbc=xy. Berk. From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Thu, 3 Apr 2008 11:55:22 +0800 Subject: [gmx-users] difference between pbc = full and pbc =xy Dear all, I want to simulate an infinite inorganic surface in gmx 3.3.3 recently. As I know, pbc = full is required for the bonded interaction on the edges. When I check the newly CVS version, a new set named pbc = xy is implemented. I wonder if there is something different between the two sets. Thanks in advance. ___ 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/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080404/99266df8/attachment-0001.html -- Message: 2 Date: Fri, 04 Apr 2008 08:08:44 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] genion problem: is replacing 84 water molecules instead of 200 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Subhrangshu Supakar wrote: Hi All !! I have defined my own system which contains 200 water molecules, which I can see in the .gro file. Then I created the .tpr file for 200 steps to steep. In the confout file I can again see the 200 water molecules. But When I am trying to replace the 200 water molecules with 200 Na+ GROMACS is complaining: genion -h is your friend. check the -rmin option. Replacing solvent molecule 144 (atom 4632) with Na Replacing solvent molecule 193 (atom 4779) with Na Replacing solvent molecule 49 (atom 4347) with Na Replacing solvent molecule 84 (atom 4452) with Na --- Program genion, VERSION 3.3.2 Source code file: gmx_genion.c, line: 84 Fatal error: No more replaceable solvent! --- It is replacing 84 water molecules only (I used genion for this) Can any body help me? Thanx in advance. Subhrangshu Supakar ___ 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
Re: [gmx-users] Re: gmx-users Digest, Vol 48, Issue 9
You are going to want to do some thorough reading through tutorial materials to start. May I suggest the following links: http://wiki.gromacs.org/index.php/Beginners http://wiki.gromacs.org/index.php/Category:Tutorials -Justin Quoting Collins Nganou [EMAIL PROTECTED]: Dear all greeting I am a new user in gromacs . To begin, I need to know how to generate date for simple water molecule and observe vibrational modes. I use this command as well as read in the manual: pdb2gmx -f prot.pdb -o prot.gro -p prot.top but when I choose ff 43a1 Opening library file /usr/share/gromacs/top/ffG43a1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading prot.pdb... I have this error: Program pdb2gmx, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: prot.pdb On Fri, Apr 4, 2008 at 12:00 PM, [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubI ascribe 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. RE: difference between pbc = full and pbc =xy (Berk Hess) 2. Re: genion problem: is replacing 84 water molecules instead of 200 (David van der Spoel) 3. Re: Test-set problem with Gromacs 3.3.3 (David van der Spoel) -- Message: 1 Date: Fri, 4 Apr 2008 03:50:40 +0200 From: Berk Hess [EMAIL PROTECTED] Subject: RE: [gmx-users] difference between pbc = full and pbc =xy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi, All options are described in share/html/online/mdp_opt.html pbc=xy is what you would (probably) guess pbc in x and y only. pbc=full is replaced by periodic_molecules, such that it can also be used with pbc=xy. Berk. From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Thu, 3 Apr 2008 11:55:22 +0800 Subject: [gmx-users] difference between pbc = full and pbc =xy Dear all, I want to simulate an infinite inorganic surface in gmx 3.3.3 recently. As I know, pbc = full is required for the bonded interaction on the edges. When I check the newly CVS version, a new set named pbc = xy is implemented. I wonder if there is something different between the two sets. Thanks in advance. ___ 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/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080404/99266df8/attachment-0001.html -- Message: 2 Date: Fri, 04 Apr 2008 08:08:44 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] genion problem: is replacing 84 water molecules instead of 200 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Subhrangshu Supakar wrote: Hi All !! I have defined my own system which contains 200 water molecules, which I can see in the .gro file. Then I created the .tpr file for 200 steps to steep. In the confout file I can again see the 200 water molecules. But When I am trying to replace the 200 water molecules with 200 Na+ GROMACS is complaining: genion -h is your friend. check the -rmin option. Replacing solvent molecule 144 (atom 4632) with Na Replacing solvent molecule 193 (atom 4779) with Na Replacing solvent molecule 49 (atom 4347) with Na Replacing solvent molecule 84 (atom 4452) with Na --- Program genion, VERSION 3.3.2 Source code file: gmx_genion.c, line: 84 Fatal error: No more replaceable solvent! --- It is replacing 84 water molecules only (I
RE: [gmx-users] angle analysis
you mah try to use VMD progam for trajectory analysis. In this program, you can visuluaze the change of bond angle through the simulation. Zuzana Benkova [EMAIL PROTECTED] schrieb: Dear GMX users, I want to analyse th ebond angle. I have used mk_angndx -s md1.tpr -n angle.ndx to prepare an index for g_angle. After g_angle -f md1.xtc -s md1.tpr -n angle.ndx I have obtained Software inconsistency error: Not supported in get_stx_coordnum Most likely this is a trivial question and I did some stupid mistake but I would be thankful for help. Thank you in advance Zuzana ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Gesendet von Yahoo! Mail. Dem pfiffigeren Posteingang.___ 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] To the GMX developers-distance restraints
To the GMX developers. Hi! I am attempting to perform distance restrained energy minimization and I have a specific doubt regarding the define parameter in em.mdp. To specify distance restraints I include disre= simple in the em.mdp file. Do I need to specify some thing like define = -DDISRES? I have not seen some thing like this in the gromacs manual but I was going thro the GMX discussion list and seen some folks define distance restraints as define = -DDISRES. I am under the impression that by specifying disre=simple I automatically turn on distance restraints. Also I saw one person had gen_vel=yes in em.mdp is this option possible . Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ 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] To the GMX developers-distance restraints
jayant james wrote: To the GMX developers. Hi! I am attempting to perform distance restrained energy minimization and I have a specific doubt regarding the define parameter in em.mdp. To specify distance restraints I include disre= simple in the em.mdp file. Do I need to specify some thing like define = -DDISRES? Only if you've set up your distance restraints section bracketed by an #ifdef DISRES ... #endif pair... see http://wiki.gromacs.org/index.php/include_file_mechanism I have not seen some thing like this in the gromacs manual but I was going thro the GMX discussion list and seen some folks define distance restraints as define = -DDISRES. I am under the impression that by specifying disre=simple I automatically turn on distance restraints. ... but only if they're defined. See manual section 4.3.4 Also I saw one person had gen_vel=yes in em.mdp is this option possible . Of course, but it's irrelevant for EM. If you haven't yet worked out what gen_vel does, then I suspect you need to do some more tutorial material and/or background reading before you worry about distance restraints, etc. 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] restraints or constraints over two molecules
Please note a new method for simulating large-scale conformational changes that take place over longer-than- molecular dynamics time scales at http://www.biophysj.org/cgi/rapidpdf/biophysj.107.118778v1.pdf The difference between this and other steering methods is that it is designed to follow more closely the microscopically reversible ensemble of paths that pertain when conformational changes take place at constant temperature. It is implemented in Gromacs and we are happy to share the code patch with users (and/or with the Gromacs developers for inserting in the next version of Gromacs)--only ask for a citation in return. Requests should go to Jay Mashl ([EMAIL PROTECTED]). Eric At 07:04 AM 4/2/2008, you wrote: Hi, We still need an elegant solution for this problem. Currently the only option is to merge the two moleculetype definitions into one. Or if you are also happy with an harmonic restraint, you can use the pull code. Berk. -- Date: Wed, 2 Apr 2008 15:53:19 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] restraints or constraints over two molecules hi, i want to ask if there is a possibility to make distance restraints or contraints over two molecules? till now i have two .itp files (one for each molecule) and i include them with 'inculde ...itp . after that i have [ system ] and [ molecules ] (with my two molecules) and then [ distance_restraints ] respectively [ contraints ]. but in both cases i get after grompp: [ file info.top, line 14 ]: Atom index (6) in distance_restraints out of bounds (1-5). so i think the problem is that i have two molecules. but is there probably another way to get this work?!? thanks for an answer. thomas schlesier ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Express yourself instantly with MSN Messenger! http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/MSN Messenger ___ 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 - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong. ---Arthur C. Clarke ___ 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] RMSD VS. parallel simulation
Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. Best regards, 2008-4-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ 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] RMSD VS. parallel simulation
DeChang Li wrote: Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? MD allows you to observe an ensemble (usually at or approaching equilibrium) over time. Any single point of that time isn't any more significant than any other. So you should expect any pair of points in different simulations (which had their velocities generated with different random numbers, right?) to generally give different values for observables, and for that not to mean anything much. Distributions of observables over long enough periods of time should be the same, however. In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. If you've done an equilibration or EM, the structure can have changed during that. 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
