Re: [gmx-users] Hydrogen bond tutorial
leila karami wrote: Dear all I want to do Hydrogen bond analysis for my MD data (protein-dna interaction). If anybody know the tutorial regarding that, please let me know. Any help will highly appreciated! Start with the manual and g_hbond -h, and come back with a more focused question. There isn't going to be detailed tutorials for every single task you can imagine, but certainly with the references provided you should be able to make a reasonable attempt at whatever analysis you're trying to do. If it doesn't work, then post what you're doing and what you want to be doing to get some advice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] H2 topology
011013021-Jyotsna wrote: Dear Mark, Thank you very much for your suggestions. In the enzyme I am trying to simulate , I need to add 100 H2 molecules (H2+dummy). when I tried adding H2 through genion , i came to know genion supports only monoatomic molecules. My aim is to replace 100 water molecules randomly by H2. How should I go about it? genconf -ci -Justin With warm regards Jyotsna , On Tue, 02 Feb 2010 16:51:19 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* On 02/02/10 14:23, 011013021-Jyotsna wrote: Dear David, Thank you very much for your help. As per the literature am following , it is mentioned that the bond distance used is 0.7 Angstrom. Where do I incorporate the bond distance parameter in the topology file? See example in chapter 5 of the manual. The problem am facing is that , I am not very clear as to if the distance is between the two Hydrogen atoms of btween the dummy atom and each of the Hydrogen atoms in either side, in which case the total distance becomes 1.4 A. Surely the text of the original article is more clear than that. In any case, from where did you get the number 0.7439756 in your topology? When i mention the bond distance in the topology file , should it be placed under Bond or constraint? The article surely specifies the nature of the bonded interaction. Work out what that is, and then consider the tables in section 5.7.1. Science in general and computational science in particular is very exacting. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a Molecular hydrogen Topology with a dummy atom in between in the simulation in order to study the path of hydrogen in it.The problem is , the topology file I built induces many errors when i come to the energy minimization step. The version of gromacs I am using is 4.0. The topology file I built is as follows [ moleculetype ] ;name nrexcl H2 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass ; total charge 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00 3 DUM 1 H2 DUM 1 -0.950 0.000 [ virtual_sites2 ] ; Site from funct a 3 1 2 1 0.7439756 When ever I insert the hydrogen+dummy atom topology in the protein's .gro file, an error is generated regarding mismatch of residues or the dummy atom having mass 0 . I would be really grateful if anyone could provide me the hydrogen molecule topology and give some pointers towards it. Please print the error message in your mail. Topology look OK, but you need to add a bond or constraint. Also the constant probably has to be 0.5 since you want the vsite in the center of the two atoms. Thank you, Jyotsna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hydrogen bond tutorial
Justin A. Lemkul skrev: leila karami wrote: Dear all I want to do Hydrogen bond analysis for my MD data (protein-dna interaction). If anybody know the tutorial regarding that, please let me know. Any help will highly appreciated! Start with the manual and g_hbond -h, and come back with a more focused question. There isn't going to be detailed tutorials for every single task you can imagine, but certainly with the references provided you should be able to make a reasonable attempt at whatever analysis you're trying to do. If it doesn't work, then post what you're doing and what you want to be doing to get some advice. -Justin And there are heaps of threads in the list archives that cover many of the problems you may run into. Erik -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] H2 topology
I think Justin meant genbox -ci Tom Justin A. Lemkul wrote: 011013021-Jyotsna wrote: Dear Mark, Thank you very much for your suggestions. In the enzyme I am trying to simulate , I need to add 100 H2 molecules (H2+dummy). when I tried adding H2 through genion , i came to know genion supports only monoatomic molecules. My aim is to replace 100 water molecules randomly by H2. How should I go about it? genconf -ci -Justin With warm regards Jyotsna , On Tue, 02 Feb 2010 16:51:19 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* On 02/02/10 14:23, 011013021-Jyotsna wrote: Dear David, Thank you very much for your help. As per the literature am following , it is mentioned that the bond distance used is 0.7 Angstrom. Where do I incorporate the bond distance parameter in the topology file? See example in chapter 5 of the manual. The problem am facing is that , I am not very clear as to if the distance is between the two Hydrogen atoms of btween the dummy atom and each of the Hydrogen atoms in either side, in which case the total distance becomes 1.4 A. Surely the text of the original article is more clear than that. In any case, from where did you get the number 0.7439756 in your topology? When i mention the bond distance in the topology file , should it be placed under Bond or constraint? The article surely specifies the nature of the bonded interaction. Work out what that is, and then consider the tables in section 5.7.1. Science in general and computational science in particular is very exacting. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a Molecular hydrogen Topology with a dummy atom in between in the simulation in order to study the path of hydrogen in it.The problem is , the topology file I built induces many errors when i come to the energy minimization step. The version of gromacs I am using is 4.0. The topology file I built is as follows [ moleculetype ] ;name nrexcl H2 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass ; total charge 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00 3 DUM 1 H2 DUM 1 -0.950 0.000 [ virtual_sites2 ] ; Site from funct a 3 1 2 1 0.7439756 When ever I insert the hydrogen+dummy atom topology in the protein's .gro file, an error is generated regarding mismatch of residues or the dummy atom having mass 0 . I would be really grateful if anyone could provide me the hydrogen molecule topology and give some pointers towards it. Please print the error message in your mail. Topology look OK, but you need to add a bond or constraint. Also the constant probably has to be 0.5 since you want the vsite in the center of the two atoms. Thank you, Jyotsna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] H2 topology
Thomas Piggot wrote: I think Justin meant genbox -ci Indeed, that is correct! Thanks for pointing that out. I know I shouldn't reply in the morning before I am thoroughly caffeinated... -Justin Tom Justin A. Lemkul wrote: 011013021-Jyotsna wrote: Dear Mark, Thank you very much for your suggestions. In the enzyme I am trying to simulate , I need to add 100 H2 molecules (H2+dummy). when I tried adding H2 through genion , i came to know genion supports only monoatomic molecules. My aim is to replace 100 water molecules randomly by H2. How should I go about it? genconf -ci -Justin With warm regards Jyotsna , On Tue, 02 Feb 2010 16:51:19 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* On 02/02/10 14:23, 011013021-Jyotsna wrote: Dear David, Thank you very much for your help. As per the literature am following , it is mentioned that the bond distance used is 0.7 Angstrom. Where do I incorporate the bond distance parameter in the topology file? See example in chapter 5 of the manual. The problem am facing is that , I am not very clear as to if the distance is between the two Hydrogen atoms of btween the dummy atom and each of the Hydrogen atoms in either side, in which case the total distance becomes 1.4 A. Surely the text of the original article is more clear than that. In any case, from where did you get the number 0.7439756 in your topology? When i mention the bond distance in the topology file , should it be placed under Bond or constraint? The article surely specifies the nature of the bonded interaction. Work out what that is, and then consider the tables in section 5.7.1. Science in general and computational science in particular is very exacting. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a Molecular hydrogen Topology with a dummy atom in between in the simulation in order to study the path of hydrogen in it.The problem is , the topology file I built induces many errors when i come to the energy minimization step. The version of gromacs I am using is 4.0. The topology file I built is as follows [ moleculetype ] ;name nrexcl H2 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass ; total charge 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00 3 DUM 1 H2 DUM 1 -0.950 0.000 [ virtual_sites2 ] ; Site from funct a 3 1 2 1 0.7439756 When ever I insert the hydrogen+dummy atom topology in the protein's .gro file, an error is generated regarding mismatch of residues or the dummy atom having mass 0 . I would be really grateful if anyone could provide me the hydrogen molecule topology and give some pointers towards it. Please print the error message in your mail. Topology look OK, but you need to add a bond or constraint. Also the constant probably has to be 0.5 since you want the vsite in the center of the two atoms. Thank you, Jyotsna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Remove my email
Please remove my email. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energy via residue
Hi all, How do i obtain the protein van der waals and electrostatic energies with bilayer via residue? highly appreciate!! Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Remove my email
mon...@lncc.br wrote: Please remove my email. Per the footer of the message you just sent: Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy via residue
afsaneh maleki wrote: Hi all, How do i obtain the protein van der waals and electrostatic energies with bilayer via residue? Set the appropriate energygrps in the .mdp file and use mdrun -rerun. Note that if you specify lots of groups you will have that number, squared, written to the energy file. -Justin highly appreciate!! Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Buckingham to Lennard-Jones (Matteus Lindgren)
On Feb 2, 2010, at 2:24 PM, Matteus Lindgren wrote: Ok thanks, sounds interesting but I think I need some more details about how to run with L-J and Buckingham at the same time even though I have read the manual. You want to use LJ for some pairs and Buckingham for others ? or the two together ? It is as simple as using different LJ for different pairs! You just have to tell what type of potential eacj pair is using! Or do I miss something. On a side note, it seems sigeps can only convert from L-J to Buckingham not the other way around. In addition, the fit of the two potentials does not seem to be very good except in the tail of the functions. Shouldn't the minima be prioritized? Instead of fitting you could use tabulated potentials which would not alter your potential form ... Regards Matteus Lindgren Matteus Lindgren, graduate student Department of Chemistry, Umee University SE-901 87 Umee, Sweden Phone: +46 (0)90-7865368 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] last line in .gro file
Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? Thanks, vishal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Checkpointing
We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt -deffnm md) I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] [OT] Software package for discontinuous molecular dynamics? (DMD)
David van der Spoel ha scritto: On 2/1/10 4:32 PM, ms wrote: Hi, Sorry for the offtopic but Google/literature quick search is not helping and I'd like to have some more informed opinion. To my understanding, GROMACS isn't capable of discontinuous molecular dynamics. Is there any more-or-less standard software package for that? thank you! m. Can you be more specific please? Uhm, in what meaning? I was pondering about using DMD for use with a coarse-grained model and I wondered if there is a standard package for that. Don't know how to be more specific, what is unclear in my question? thanks, M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Dear Justin, I am trying to set up calculations for a cellulose structure. The allomorph of cellulose which I want to study has a monoclinic structure. I have a .cif file of the XRD structure. I think the better question to ask is how can I make input files using that. thanks vishal On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Vishal Agarwal wrote: Dear Justin, I am trying to set up calculations for a cellulose structure. The allomorph of cellulose which I want to study has a monoclinic structure. I have a .cif file of the XRD structure. I think the better question to ask is how can I make input files using that. That is a far more complex question. There are numerous posts in the list archive regarding preparing input for polymeric systems, so please do search the list archive. I helped one user set up a polyethylene system some time ago, so that may help out. You'll have to familiarize yourself with .rtp entry construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to get it to work though. There are lots of resources in the manual and on the Gromacs wiki pages to get you started. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards
[gmx-users] Replica Exchange MD on more than 64 processors
Dear list I recently came up with a problem concerning a replica exchange simulation. The simulation is run with gromacs-mpi in Version 4.0.7 compiled with following flags --enable-threads --enable-mpi --with-fft=mkl -enable-double, intel compiler version 11.0 mvapich version 1.1.0 mkl version 10.1 The program is working fine in this cluster evironment consisting of 32 nodes with 8 processors and 32GB each. I've already run several simulations using the MPI feature. It seems that I stuck in a similar problem that was already announced on this list by bharat v. adkar in december 2009 without an eventual solution: http://www.mail-archive.com/gmx-users@gromacs.org/msg27175.html I am doing a replica exchange simulation on a simulation box with 5000 molecules (81 atoms each) and 4 different temperatures. The simulation runs nicely with 64 processors (8 nodes) but stops with an error message on 128 processors (16 nodes). Taking the following four points into account: 1. every cluster node has at least 28GB memory in a usable way available 2. the system I am working with should only use 5000*81*900B=347.614MB (according to the FAQ) 3. even if every replica (4) is run on the same node the memory usage should be less than 2GB 4. the simulation works fine with 64 processors it seems to me the following error --- Program mdrun, VERSION 4.0.7 Source code file: smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0xae70b7b0 (called from file ns.c, line 503) --- has to be caused by another issue than missing memory. I am wondering if there is anyone else who is still facing the same problem or has already found a solution for this issue. Kind regards Sebastian -- _ Sebastian BreuersTel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für ChemieDepartment Chemistry Organische Chemieuniversity of Cologne Greinstr. 4 Greinstr. 4 D-50939 Köln D-50939 Cologne, Federal Rep. of Germany _ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Replica Exchange MD on more than 64 processors
Hi, One issue could be MPI memory usage. I have noticed that many MPI implementations use an amount of memory per process that is quadratic (!) in the number of processes involved. This can quickly get out of hand. But 28 GB is a lot of memory. One thing that might help slightly is to not use double precision, which is almost never required. This will also make your simulations a factor 1.4 faster. Berk Date: Tue, 2 Feb 2010 18:55:37 +0100 From: breue...@uni-koeln.de To: gmx-users@gromacs.org Subject: [gmx-users] Replica Exchange MD on more than 64 processors Dear list I recently came up with a problem concerning a replica exchange simulation. The simulation is run with gromacs-mpi in Version 4.0.7 compiled with following flags --enable-threads --enable-mpi --with-fft=mkl -enable-double, intel compiler version 11.0 mvapich version 1.1.0 mkl version 10.1 The program is working fine in this cluster evironment consisting of 32 nodes with 8 processors and 32GB each. I've already run several simulations using the MPI feature. It seems that I stuck in a similar problem that was already announced on this list by bharat v. adkar in december 2009 without an eventual solution: http://www.mail-archive.com/gmx-users@gromacs.org/msg27175.html I am doing a replica exchange simulation on a simulation box with 5000 molecules (81 atoms each) and 4 different temperatures. The simulation runs nicely with 64 processors (8 nodes) but stops with an error message on 128 processors (16 nodes). Taking the following four points into account: 1. every cluster node has at least 28GB memory in a usable way available 2. the system I am working with should only use 5000*81*900B=347.614MB (according to the FAQ) 3. even if every replica (4) is run on the same node the memory usage should be less than 2GB 4. the simulation works fine with 64 processors it seems to me the following error --- Program mdrun, VERSION 4.0.7 Source code file: smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0xae70b7b0 (called from file ns.c, line 503) --- has to be caused by another issue than missing memory. I am wondering if there is anyone else who is still facing the same problem or has already found a solution for this issue. Kind regards Sebastian -- _ Sebastian BreuersTel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für ChemieDepartment Chemistry Organische Chemieuniversity of Cologne Greinstr. 4 Greinstr. 4 D-50939 Köln D-50939 Cologne, Federal Rep. of Germany _ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Replica Exchange MD on more than 64 processors
Dear list I recently came up with a problem concerning a replica exchange simulation. The simulation is run with gromacs-mpi in Version 4.0.7 compiled with following flags --enable-threads --enable-mpi --with-fft=mkl -enable-double, intel compiler version 11.0 mvapich version 1.1.0 mkl version 10.1 The program is working fine in this cluster evironment consisting of 32 nodes with 8 processors and 32GB each. I've already run several simulations using the MPI feature. It seems that I stuck in a similar problem that was already announced on this list by bharat v. adkar in december 2009 without an eventual solution: http://www.mail-archive.com/gmx-users@gromacs.org/msg27175.html I am doing a replica exchange simulation on a simulation box with 5000 molecules (81 atoms each) and 4 different temperatures. The simulation runs nicely with 64 processors (8 nodes) but stops with an error message on 128 processors (16 nodes). Taking the following four points into account: 1. every cluster node has at least 28GB memory in a usable way available 2. the system I am working with should only use 5000*81*900B=347.614MB (according to the FAQ) 3. even if every replica (4) is run on the same node the memory usage should be less than 2GB 4. the simulation works fine with 64 processors it seems to me the following error --- Program mdrun, VERSION 4.0.7 Source code file: smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0xae70b7b0 (called from file ns.c, line 503) --- has to be caused by another issue than missing memory. I am wondering if there is anyone else who is still facing the same problem or has already found a solution for this issue. Kind regards Sebastian -- _ Sebastian BreuersTel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für ChemieDepartment Chemistry Organische Chemieuniversity of Cologne Greinstr. 4 Greinstr. 4 D-50939 Köln D-50939 Cologne, Federal Rep. of Germany _ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Dear Justin, Thanks for replying. You mentioned that gromacs supports triclinic structure. Can you tell me what will be the box parameters for triclinic structure of cell parameters a, b, c and angles alpha, beta and gama. Thanks in advance Vishal On Tue, Feb 2, 2010 at 12:30 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, I am trying to set up calculations for a cellulose structure. The allomorph of cellulose which I want to study has a monoclinic structure. I have a .cif file of the XRD structure. I think the better question to ask is how can I make input files using that. That is a far more complex question. There are numerous posts in the list archive regarding preparing input for polymeric systems, so please do search the list archive. I helped one user set up a polyethylene system some time ago, so that may help out. You'll have to familiarize yourself with .rtp entry construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to get it to work though. There are lots of resources in the manual and on the Gromacs wiki pages to get you started. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] last line in .gro file
Hi, Since any unit cell can be formulated as a triclinic cell, the monoclinic cell is indeed supported. By definition it has two 90 degree angles and one that is not 90 degrees. The box vectors can be of different lengths. You'll have to do the math and reading yourself to find out how this translates to a .gro box. The manual is your friend here. Good luck, Erik Vishal Agarwal skrev: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Hi Vishal, Here is a python function that generates a triclinic representation given a definition with lengths and angles. The argument L is a tuple or list containing the lengths and angles. def triclinic(L): B = [[0,0,0],[0,0,0],[0,0,0]] x, y, z, a, b, c = L[:6] B[0][0] = x if a == 90 and b == 90 and c == 90: B[1][1] = y B[2][2] = z else: a = a*pi/180 b = b*pi/180 c = c*pi/180 B[1][0] = y*cos(c) B[1][1] = y*sin(c) B[2][0] = z*cos(b) B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c) B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2) return B Hope it helps, Tsjerk On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Since any unit cell can be formulated as a triclinic cell, the monoclinic cell is indeed supported. By definition it has two 90 degree angles and one that is not 90 degrees. The box vectors can be of different lengths. You'll have to do the math and reading yourself to find out how this translates to a .gro box. The manual is your friend here. Good luck, Erik Vishal Agarwal skrev: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] [OT] Software package for discontinuous molecular dynamics? (DMD)
On 2/2/10 4:43 PM, ms wrote: David van der Spoel ha scritto: On 2/1/10 4:32 PM, ms wrote: Hi, Sorry for the offtopic but Google/literature quick search is not helping and I'd like to have some more informed opinion. To my understanding, GROMACS isn't capable of discontinuous molecular dynamics. Is there any more-or-less standard software package for that? thank you! m. Can you be more specific please? Uhm, in what meaning? I was pondering about using DMD for use with a coarse-grained model and I wondered if there is a standard package for that. Don't know how to be more specific, what is unclear in my question? thanks, M. What is discrete MD? -- David. David van der Spoel, PhD, Professor of Biology 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 sp...@xray.bmc.uu.sesp...@gromacs.org http://xray.bmc.uu.se/~spoel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] [OT] Software package for discontinuous molecular dynamics? (DMD)
David van der Spoel ha scritto: On 2/2/10 4:43 PM, ms wrote: David van der Spoel ha scritto: On 2/1/10 4:32 PM, ms wrote: Hi, Sorry for the offtopic but Google/literature quick search is not helping and I'd like to have some more informed opinion. To my understanding, GROMACS isn't capable of discontinuous molecular dynamics. Is there any more-or-less standard software package for that? thank you! m. Can you be more specific please? Uhm, in what meaning? I was pondering about using DMD for use with a coarse-grained model and I wondered if there is a standard package for that. Don't know how to be more specific, what is unclear in my question? thanks, M. What is discrete MD? Uh, sorry. Probably references know better than me: http://pubs.acs.org/doi/full/10.1021/ja0539140 is an example of it applied to proteins. (I am looking for reviews on the subject but can't find recent ones) It is a coarse-grained technique for use with discontinuous potentials, which roughly speaking uses collision detection instead of fine-grained potential calculation: In a discontinuous molecular dynamics (DMD) simulation, particles collide when they arrive at a discontinuity in the potential, that is, the hard-sphere diameter or the square-well width. Between collisions, particles move with linear trajectories, making DMD simulations much faster than traditional molecular dynamics simulations with continuous potentials which require a small integration time step. The postcollision velocities of particles in DMD are found by solving the collision dynamics equations analytically. (from http://pubs.acs.org/doi/full/10.1021/la049267s ) I don't know much about it, but I was curious and I wanted to know if there was a package for it (or if Gromacs was capable of it). thanks! m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Checkpointing
- Original Message - From: Jack Shultz j...@drugdiscoveryathome.com Date: Wednesday, February 3, 2010 2:36 Subject: [gmx-users] Checkpointing To: Discussion list for GROMACS users gmx-users@gromacs.org, Andrey Voronkov a...@drugdiscoveryathome.com We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - deffnm md) If you're using this input line always, then you're getting what you're asking for - an mdrun that begins from the state in md.cpt. Since you're never updating that, it doesn't change. Try not stipulating different -cpo and -cpi and see what the native coping mechanism is. Otherwise, you'll have to write a bunch of scripting logic to decide which .cpt to use each restart. Mark I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hessian Matrix
Hi everyone, I tried to use mdrun to get the .mtx file, but it does not work, I mean...no mtx file output. Below is the command I used in the scripts of my last two trial. 1) ## To run on 16 cpus #PBS -l nodes=2:ppn=8 ## program to run mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em 2) ## program to run mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx Thanks and best, lina winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hessian Matrix
#ZHAO LINA# wrote: Hi everyone, I tried to use mdrun to get the .mtx file, but it does not work, I mean...no mtx file output. Below is the command I used in the scripts of my last two trial. 1) ## To run on 16 cpus #PBS -l nodes=2:ppn=8 ## program to run mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em 2) ## program to run mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx Probably because the Hessian is only relevant when doing normal mode calculations (or perhaps L-BFGS minimization). I suspect that if you're not using the nm integrator, then you're not going to get the Hessian. -Justin Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Restrained Molecule is Moving
Hello, I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) of my box of dimensions 3.2418 X 3.2418 X 3.2418 nm. The box is also full of 253 THF molecules. I added the following to the bottom of my .itp file: #ifdef POSRES #include posre_Na+.itp #endif I wrote the posre_Na+.itp file myself, it just includes the position restraints for Na+, which is atom 1 in my .gro file, and my posre_Na+.itp file deals with atom 1. The force constants are all 1000. Under the .mdp file, I also made sure that define = -DPOSRES. I get no errors when things run, but I do get my Na+ moving around. After I do energy minimization, Na+ ends up at the position (0.373, 1.504, 1.226). I also do not notice anything about position restraints appearing in my .log file afterwards. I really appreciate the help. Thank you, Jenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Restrained Molecule is Moving
Jennifer Casey wrote: Hello, I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) of my box of dimensions 3.2418 X 3.2418 X 3.2418 nm. The box is also full of 253 THF molecules. I added the following to the bottom of my .itp file: #ifdef POSRES #include posre_Na+.itp #endif I wrote the posre_Na+.itp file myself, it just includes the position restraints for Na+, which is atom 1 in my .gro file, and my posre_Na+.itp file deals with atom 1. The force constants are all 1000. It does not matter so much whether the atom number is the same, but rather if the position restraint definition directly follows the [moleculetype] definition of Na+ in your system. Without seeing your topology file, there's no way to know if you've placed the position restraint file in the right place. -Justin Under the .mdp file, I also made sure that define = -DPOSRES. I get no errors when things run, but I do get my Na+ moving around. After I do energy minimization, Na+ ends up at the position (0.373, 1.504, 1.226). I also do not notice anything about position restraints appearing in my .log file afterwards. I really appreciate the help. Thank you, Jenny -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Restrained Molecule is Moving
Jennifer Casey wrote: Thank you so much for your quick response. I have attached my .itp, and .top files. I think that the if statement was originally in the wrong spot, but after changing in and running an energy minimization, there is still some drifting - the Na+ moves to (0.566, 1.559, 1.586) from (0.486, 1.621, 1.621). Maybe this is normal amount of drift? Possibly. Position restraints only specify a force constant to oppose motion, not completely fix coordinates, so some movement is possible. To test, you could specify an extremely high force constant (10 or more) in the posre.itp file and see if the position changes any less. -Justin Thanks again, Jenny On Tue, Feb 2, 2010 at 6:01 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jennifer Casey wrote: Hello, I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) of my box of dimensions 3.2418 X 3.2418 X 3.2418 nm. The box is also full of 253 THF molecules. I added the following to the bottom of my .itp file: #ifdef POSRES #include posre_Na+.itp #endif I wrote the posre_Na+.itp file myself, it just includes the position restraints for Na+, which is atom 1 in my .gro file, and my posre_Na+.itp file deals with atom 1. The force constants are all 1000. It does not matter so much whether the atom number is the same, but rather if the position restraint definition directly follows the [moleculetype] definition of Na+ in your system. Without seeing your topology file, there's no way to know if you've placed the position restraint file in the right place. -Justin Under the .mdp file, I also made sure that define = -DPOSRES. I get no errors when things run, but I do get my Na+ moving around. After I do energy minimization, Na+ ends up at the position (0.373, 1.504, 1.226). I also do not notice anything about position restraints appearing in my .log file afterwards. I really appreciate the help. Thank you, Jenny -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Hi Tsjerk, Thanks for replying. I was going through the pdb format dcoument on the PDB webpage. I found that the box corresponds to the following: a b(cos(gama)) c(cos(beta)) 0 b(sin(gama)) c(cos(alpha) - cos(beta) cos(gama) / sin(gama) 00 V/(ab sin(gama)) where V = abc(1 - (cos(alpha))^2 - (cos(beta))^2 - (cos(gama))^2+ 2cos(alpha) cos(beta) cos(gama))^1/2 This corresponds to general form in representing these vectors. The following code also desolves to this form. Thank you again. Best, Vishal P.S. I thank all who have replied to this mail. On Tue, Feb 2, 2010 at 3:44 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vishal, Here is a python function that generates a triclinic representation given a definition with lengths and angles. The argument L is a tuple or list containing the lengths and angles. def triclinic(L): B = [[0,0,0],[0,0,0],[0,0,0]] x, y, z, a, b, c = L[:6] B[0][0] = x if a == 90 and b == 90 and c == 90: B[1][1] = y B[2][2] = z else: a = a*pi/180 b = b*pi/180 c = c*pi/180 B[1][0] = y*cos(c) B[1][1] = y*sin(c) B[2][0] = z*cos(b) B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c) B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2) return B Hope it helps, Tsjerk On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Since any unit cell can be formulated as a triclinic cell, the monoclinic cell is indeed supported. By definition it has two 90 degree angles and one that is not 90 degrees. The box vectors can be of different lengths. You'll have to do the math and reading yourself to find out how this translates to a .gro box. The manual is your friend here. Good luck, Erik Vishal Agarwal skrev: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or
[gmx-users] Re: Hessian Matrix
Hi, I just simply did a change in .mdp file. Now the integrator = nm after grompp, 1) below is the error of mdrun -s em.tpr -mtx em.mtx Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 4118944041 elements of size 4 for full_matrix (called from file ../../../../src/mdlib/minimize.c, line 2219) 2) Seems the one run in cluster choked there like this in md.log. Linking all bonded interactions to atoms There are 2106 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.76 nm Y 1.07 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.000 nm two-body bonded interactions (-rdd) 1.000 nm multi-body bonded interactions (-rdd) 1.000 nm Thanks for further suggestion, lina #ZHAO LINA# wrote: Hi everyone, I tried to use mdrun to get the .mtx file, but it does not work, I mean...no mtx file output. Below is the command I used in the scripts of my last two trial. 1) ## To run on 16 cpus #PBS -l nodes=2:ppn=8 ## program to run mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em 2) ## program to run mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx Probably because the Hessian is only relevant when doing normal mode calculations (or perhaps L-BFGS minimization). I suspect that if you're not using the nm integrator, then you're not going to get the Hessian. -Justin Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Hessian Matrix
#ZHAO LINA# wrote: Hi, I just simply did a change in .mdp file. Now the integrator = nm after grompp, 1) below is the error of mdrun -s em.tpr -mtx em.mtx Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 4118944041 elements of size 4 for full_matrix (called from file ../../../../src/mdlib/minimize.c, line 2219) You might want to take a step back and consider what you're doing. I didn't suggest you use the nm integrator ad hoc to get some arbitrary output. You have to understand what normal modes calculations are before you just dive in and try them. They actually require quite a bit of finesse: http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis You're asking mdrun to do a huge amount of calculation, which your system may not be able to handle. Perhaps if you can define why (you think) you need a Hessian you'll get some more specific advice. 2) Seems the one run in cluster choked there like this in md.log. Linking all bonded interactions to atoms There are 2106 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.76 nm Y 1.07 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.000 nm two-body bonded interactions (-rdd) 1.000 nm multi-body bonded interactions (-rdd) 1.000 nm I don't understand how this is related. These are normal messages related to domain decomposition. -Justin Thanks for further suggestion, lina #ZHAO LINA# wrote: Hi everyone, I tried to use mdrun to get the .mtx file, but it does not work, I mean...no mtx file output. Below is the command I used in the scripts of my last two trial. 1) ## To run on 16 cpus #PBS -l nodes=2:ppn=8 ## program to run mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em 2) ## program to run mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx Probably because the Hessian is only relevant when doing normal mode calculations (or perhaps L-BFGS minimization). I suspect that if you're not using the nm integrator, then you're not going to get the Hessian. -Justin Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Checkpointing
I will try it without the checkpointing flags. If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists. On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Jack Shultz j...@drugdiscoveryathome.com Date: Wednesday, February 3, 2010 2:36 Subject: [gmx-users] Checkpointing To: Discussion list for GROMACS users gmx-users@gromacs.org, Andrey Voronkov a...@drugdiscoveryathome.com We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - deffnm md) If you're using this input line always, then you're getting what you're asking for - an mdrun that begins from the state in md.cpt. Since you're never updating that, it doesn't change. Try not stipulating different -cpo and -cpi and see what the native coping mechanism is. Otherwise, you'll have to write a bunch of scripting logic to decide which .cpt to use each restart. Mark I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMOS96 parameters in itp file obtained from PRODRG
Dear gromas users, I am new to gromacs and trying to run polyacrylate MD simulation. I obtained an itp file using PRODRG (gromos 96 force-field parameters). When I compare with the same forcefield parameters in the gromacs/top directory, they are far too off. For eg. [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.125 1340.00.125 1340.0 ; CAC OAD 2 3 20.125 1340.00.125 1340.0 ; CAC OAE 4 2 20.153 715.00.153 715.0 ; CAB CAC 4 5 20.153 715.00.153 715.0 ; CAB CAA 4 6 20.153 715.00.153 715.0 ; CAB CAG 7 6 20.153 715.00.153 715.0 ; CAH CAG 7 8 20.153 715.00.153 715.0 ; CAH CAI As I understand, the function type should be 1 and c1 values should correspond to the force constant for bond stretching. But here it corresponds to the pair wise non bond parameters as listed in the gromacs/top force-field file. Similarly, [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; OAD CAA 1 6 1 ; OAD CAG 2 7 1 ; CAC CAH 3 5 1 ; OAE CAA 3 6 1 ; OAE CAG 4 8 1 ; CAB CAI 4 11 1 ; CAB CAL 5 7 1 ; CAA CAH there are no pair terms listed here in the pairs section. [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2126.0 770.0126.0 770.0 ; OAD CAC OAE 1 2 4 2117.0 635.0117.0 635.0 ; OAD CAC CAB 3 2 4 2117.0 635.0117.0 635.0 ; OAE CAC CAB 2 4 5 2109.5 520.0109.5 520.0 ; CAC CAB CAA 2 4 6 2109.5 520.0109.5 520.0 ; CAC CAB CAG 5 4 6 2109.5 520.0109.5 520.0 ; CAA CAB CAG 4 6 7 2109.5 520.0109.5 520.0 ; CAB CAG CAH For angles also the fu term is 2 instead of 1, although the angle and the force constant parameters are correct. Similar errors are there in the dihedrals section also. This means I need to almost fully edit the itp file I got from PRODRG to proceed further. Thank you in advance for any help and please clarify whether the itp file from PRODRG is unreliable even while using GROMOS96 force field ? Thanking you, Dr. M. S Sulatha Women Scientist Chemical Engineering Dept. IIT-Madras, Chennai India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Checkpointing
On 03/02/10 15:44, Jack Shultz wrote: I will try it without the checkpointing flags. That's not quite what I said. I suggested not using *different* filenames for -cpo and -cpi. What you want is the output file from a former run to transparently become the input file for the subsequent one, and I expect GROMACS will handle this for you if you let it. Try some things and see. Mark If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists. On Tue, Feb 2, 2010 at 6:18 PM, Mark Abrahammark.abra...@anu.edu.au wrote: - Original Message - From: Jack Shultzj...@drugdiscoveryathome.com Date: Wednesday, February 3, 2010 2:36 Subject: [gmx-users] Checkpointing To: Discussion list for GROMACS usersgmx-users@gromacs.org, Andrey Voronkova...@drugdiscoveryathome.com We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - deffnm md) If you're using this input line always, then you're getting what you're asking for - an mdrun that begins from the state in md.cpt. Since you're never updating that, it doesn't change. Try not stipulating different -cpo and -cpi and see what the native coping mechanism is. Otherwise, you'll have to write a bunch of scripting logic to decide which .cpt to use each restart. Mark I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Checkpointing
So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll try this approach again. I had a little trouble doing it this way previously. I think I had trouble with the extension scripts doing it this way. On Tue, Feb 2, 2010 at 11:56 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 03/02/10 15:44, Jack Shultz wrote: I will try it without the checkpointing flags. That's not quite what I said. I suggested not using *different* filenames for -cpo and -cpi. What you want is the output file from a former run to transparently become the input file for the subsequent one, and I expect GROMACS will handle this for you if you let it. Try some things and see. Mark If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists. On Tue, Feb 2, 2010 at 6:18 PM, Mark Abrahammark.abra...@anu.edu.au wrote: - Original Message - From: Jack Shultzj...@drugdiscoveryathome.com Date: Wednesday, February 3, 2010 2:36 Subject: [gmx-users] Checkpointing To: Discussion list for GROMACS usersgmx-users@gromacs.org, Andrey Voronkova...@drugdiscoveryathome.com We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - deffnm md) If you're using this input line always, then you're getting what you're asking for - an mdrun that begins from the state in md.cpt. Since you're never updating that, it doesn't change. Try not stipulating different -cpo and -cpi and see what the native coping mechanism is. Otherwise, you'll have to write a bunch of scripting logic to decide which .cpt to use each restart. Mark I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Checkpointing
On 03/02/10 16:38, Jack Shultz wrote: So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll try this approach again. I had a little trouble doing it this way previously. I think I had trouble with the extension scripts doing it this way. I'd equilibrate, then use mdrun -cpi state and see from the timestamps where the output .cpt is, and arrange future mdrun to use that. IIRC GROMACS handles life to not lose data, but does so differently according to the presence of -append. The more things you specify on the command line, the lower the chance of you have of having work done for you, in this regard. Mark On Tue, Feb 2, 2010 at 11:56 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 03/02/10 15:44, Jack Shultz wrote: I will try it without the checkpointing flags. That's not quite what I said. I suggested not using *different* filenames for -cpo and -cpi. What you want is the output file from a former run to transparently become the input file for the subsequent one, and I expect GROMACS will handle this for you if you let it. Try some things and see. Mark If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists. On Tue, Feb 2, 2010 at 6:18 PM, Mark Abrahammark.abra...@anu.edu.au wrote: - Original Message - From: Jack Shultzj...@drugdiscoveryathome.com Date: Wednesday, February 3, 2010 2:36 Subject: [gmx-users] Checkpointing To: Discussion list for GROMACS usersgmx-users@gromacs.org, Andrey Voronkova...@drugdiscoveryathome.com We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - deffnm md) If you're using this input line always, then you're getting what you're asking for - an mdrun that begins from the state in md.cpt. Since you're never updating that, it doesn't change. Try not stipulating different -cpo and -cpi and see what the native coping mechanism is. Otherwise, you'll have to write a bunch of scripting logic to decide which .cpt to use each restart. Mark I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMOS96 parameters in itp file obtained from PRODRG
On 03/02/10 15:55, sulatha M. S wrote: Dear gromas users, I am new to gromacs and trying to run polyacrylate MD simulation. I obtained an itp file using PRODRG (gromos 96 force-field parameters). When I compare with the same forcefield parameters in the gromacs/top directory, they are far too off. For eg. [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.125 1340.0 0.125 1340.0 ; CAC OAD 2 3 2 0.125 1340.0 0.125 1340.0 ; CAC OAE 4 2 2 0.153 715.0 0.153 715.0 ; CAB CAC 4 5 2 0.153 715.0 0.153 715.0 ; CAB CAA 4 6 2 0.153 715.0 0.153 715.0 ; CAB CAG 7 6 2 0.153 715.0 0.153 715.0 ; CAH CAG 7 8 2 0.153 715.0 0.153 715.0 ; CAH CAI As I understand, the function type should be 1 and c1 values should correspond to the force constant for bond stretching. But here it corresponds to the pair wise non bond parameters as listed in the gromacs/top force-field file. Similarly, The bonded function type can have a whole range of values. See table in section 5.7.1 of the manual. That and the parameters, and the form of the target forcefield have to be considered as a whole in judging acceptability. It's quite conceivable that the same numerical values are used in a bonded interaction (in [bonds] above) and forming the parameters in non-bonded interaction (in the [atomtypes] in the ffG96XXXbon.itp file) for in this case both pairs can represent quantities whose dimensions are length and energy respectively. [ pairs ] ; ai aj fu c0, c1, ... 1 5 1 ; OAD CAA 1 6 1 ; OAD CAG 2 7 1 ; CAC CAH 3 5 1 ; OAE CAA 3 6 1 ; OAE CAG 4 8 1 ; CAB CAI 4 11 1 ; CAB CAL 5 7 1 ; CAA CAH there are no pair terms listed here in the pairs section. Some forcefields generate these solely from the [atomtype] data. [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 126.0 770.0 126.0 770.0 ; OAD CAC OAE 1 2 4 2 117.0 635.0 117.0 635.0 ; OAD CAC CAB 3 2 4 2 117.0 635.0 117.0 635.0 ; OAE CAC CAB 2 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAB CAA 2 4 6 2 109.5 520.0 109.5 520.0 ; CAC CAB CAG 5 4 6 2 109.5 520.0 109.5 520.0 ; CAA CAB CAG 4 6 7 2 109.5 520.0 109.5 520.0 ; CAB CAG CAH For angles also the fu term is 2 instead of 1, although the angle and the force constant parameters are correct. Similar errors are there in the dihedrals section also. This means I need to almost fully edit the itp file I got from PRODRG to proceed further. Thank you in advance for any help and please clarify whether the itp file from PRODRG is unreliable even while using GROMOS96 force field ? There's no evidence of any error here. You should satisfy yourself from the contents of chapter 5 and the correct form of the GROMOS energy function that PRODRG is doing what you think it should. It looks to me like PRODRG is fine and you don't yet understand the form of what it should be producing. I suggest that you should do that learning. Whether the numerical values will be sensible for MD simulations (as distinct from being expressed in a suitable form) is quite another question. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
