Re: [gmx-users] major issue with gmx-4.0.3?
I had a look at the notes ... nothing there to satisfy my concerns :)) If gmx-403 is fine on the basic MD level it is then good news. If anybody recalls some thing I would appreciate to be informed. Best, XAvier. XAvier Periole wrote: Dears, I recall the report of a major issue in gmx-4.0.3. At the time this made me put gmx403 on the side of not to be used versions. I can not find a trace of it ... anyone would remember anything? I thought the major problem was with 4.0.1 - it had something broken that caused simulations to run something like 50% slower, and hence why it is unavailable for download. There were some issues with the free energy code, missing interactions when using TIP4P, I believe, and otherwise small issues with the pull code. Complete release notes are posted on the website: http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 -Justin Thanks, XAvier. ___ 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 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 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] Re: Advantage of NPT over NVT?
If your model gives a correct fluid density with NPT, use NPT. If it does not, then use NVT. This is a quick practical guide, not not read much. :) Vitaly ___ 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] forcefield
Hi Lalitha, Zebularine is beyond the trivial. You may be able to derive something reasonable from the other bases using 'chemical intuition' (cytidine, thymidine, uracil), but it's likely that the electronic structure of the ring is too different to justify an approach like that. Likely you should perform parameterization the proper way, which is not a beginners subject. At least have a look at http://www.gromacs.org/WIKI-import/Parametrization Cheers, Tsjerk On Wed, Oct 14, 2009 at 7:30 AM, lalitha selvam hayagri...@hotmail.com wrote: Hi, I want to do simulation with the ligand called zebularine. I dont find forcefied for that. Also i read prodgr has been deprecated.. Could you please help me to find out the forcefield for the ligand zebularine. Thanks in advance lalitha Don’t fall behind. Log on to MSN India for a roundup on the world panorama ___ 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. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://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] run g_cover in parallel
Hi, I wonder if there a way to run g_cover in paralel in order to make things run faster? No. Obviously you can use -dt to reduce the number of frames you analyze. In most cases it's not the reading of frames, but the diagonalization of the covariance matrix that consumes most of the time. It might be interesting to have it MPI enabled, especially since systems are getting bigger and bigger. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://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: Advantage of NPT over NVT?
Vitaly V. Chaban wrote: If your model gives a correct fluid density with NPT, use NPT. If it does not, then use NVT. This is a quick practical guide, not not read much. :) Sounds dangerous :-) If the model produces a wrong density, you'd want to be reasonably confident your observable is not linked to the underlying cause, before just proceeding at NVT... Sounds like a really easy criticism for a reviewer to knock back a paper on. 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
Re: [gmx-users] run g_cover in parallel
Tsjerk Wassenaar wrote: Hi, I wonder if there a way to run g_cover in paralel in order to make things run faster? No. Obviously you can use -dt to reduce the number of frames you analyze. In most cases it's not the reading of frames, but the diagonalization of the covariance matrix that consumes most of the time. True, such an algorithm for N atoms over F frames is either something like O(F) or O(N^3) according to whether the I/O-and-compute phase or the diagonalization phase dominates. Once could also reduce N by coarse-graining the covariance matrix. It might be interesting to have it MPI enabled, especially since systems are getting bigger and bigger. Someone would have to identify a candidate MPI diagonalization algorithm that can be readily added. That doesn't sound like a easy algorithm to write with numerical stability :-) ScaLAPACK http://www.netlib.org/scalapack/html/scalapack_single.html might work - how about http://www.netlib.org/scalapack/single/pssyevd.f ? It would add further dependency to the build process, unless we incorporated it as with BLAS and LAPACK. 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
Re: [gmx-users] What is best way to get multiple chains?
Mark Abraham ha scritto: ms wrote: Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx This step is generating a molecular topology. You don't need a .gro - it's just a regularized coordinate file produced as a side-effect. Very much right. Thanks. - Used editconf to create translated copies Try genconf to do the replication. That should remove much of the manual labour. You would still probably need to edit in the chain IDs yourself, but that's easy work with a script or good editor. Thanks! - Stitching them together and creating the complete file, adjusting numbers etc. manually It worked well, but the chains are not recognized as *different* chains -which could be useful. Documentation says I should use another format like the pdb, but it is a bit sparse on the subject. I think I can use pdb instead of gro if needed, but does this also work when creating boxes etc.? Isn't there a way to get chain identifiers in a gro file? What is best practice? What do you want the chain identifiers for? I'm not aware of a post-pdb2gmx purpose that they might serve. This is where my naivety probably enters in: Analysis programs work on groups. If several chains are defined, can each of these count as a group? Indeed, chapter 8 doesn't explicitly say so, but... My intention is to get analysis for each chain in my system. What is best practice for that / where should I look in the docs? If your system is N identical peptides in a solvent, then best practice for generating a complete .top is to generate one for a single peptide in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a coordinate file which contains the N peptides' coordinates followed by all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] section of the original .top to match. Other solutions are possible, but require more involved use of pdb2gmx, and might indeed want chain IDs. Uh, thanks. Not sure to have understood all of it, but I will do my homework before coming back :) 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] What is best way to get multiple chains?
ms wrote: Mark Abraham ha scritto: ms wrote: Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx This step is generating a molecular topology. You don't need a .gro - it's just a regularized coordinate file produced as a side-effect. Very much right. Thanks. - Used editconf to create translated copies Try genconf to do the replication. That should remove much of the manual labour. You would still probably need to edit in the chain IDs yourself, but that's easy work with a script or good editor. Thanks! - Stitching them together and creating the complete file, adjusting numbers etc. manually It worked well, but the chains are not recognized as *different* chains -which could be useful. Documentation says I should use another format like the pdb, but it is a bit sparse on the subject. I think I can use pdb instead of gro if needed, but does this also work when creating boxes etc.? Isn't there a way to get chain identifiers in a gro file? What is best practice? What do you want the chain identifiers for? I'm not aware of a post-pdb2gmx purpose that they might serve. This is where my naivety probably enters in: Analysis programs work on groups. If several chains are defined, can each of these count as a group? Indeed, chapter 8 doesn't explicitly say so, but... My intention is to get analysis for each chain in my system. What is best practice for that / where should I look in the docs? They can, but you have to define them. If there are multiple protein chains in the system, the Gromacs tools will define them as one group - 'Protein' - and not distinguish between them. This is a rather easy problem to solve, though, without even using chain identifiers. You can create index groups based on residue numbers to define each chain, then it doesn't matter what format the coordinate file is in. For example, you can define groups like: r 1-37 r 38-299 etc. -Justin If your system is N identical peptides in a solvent, then best practice for generating a complete .top is to generate one for a single peptide in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a coordinate file which contains the N peptides' coordinates followed by all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] section of the original .top to match. Other solutions are possible, but require more involved use of pdb2gmx, and might indeed want chain IDs. Uh, thanks. Not sure to have understood all of it, but I will do my homework before coming back :) 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] What is best way to get multiple chains?
ms wrote: Mark Abraham ha scritto: ms wrote: Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx This step is generating a molecular topology. You don't need a .gro - it's just a regularized coordinate file produced as a side-effect. Very much right. Thanks. - Used editconf to create translated copies Try genconf to do the replication. That should remove much of the manual labour. You would still probably need to edit in the chain IDs yourself, but that's easy work with a script or good editor. Thanks! - Stitching them together and creating the complete file, adjusting numbers etc. manually It worked well, but the chains are not recognized as *different* chains -which could be useful. Documentation says I should use another format like the pdb, but it is a bit sparse on the subject. I think I can use pdb instead of gro if needed, but does this also work when creating boxes etc.? Isn't there a way to get chain identifiers in a gro file? What is best practice? What do you want the chain identifiers for? I'm not aware of a post-pdb2gmx purpose that they might serve. This is where my naivety probably enters in: Analysis programs work on groups. If several chains are defined, can each of these count as a group? Indeed, chapter 8 doesn't explicitly say so, but... My intention is to get analysis for each chain in my system. What is best practice for that / where should I look in the docs? make_ndx is the tool for generating such groups. If you read make_ndx -h you'll see it does indeed let you create groups based around chain IDs, but that'd (at least) require supplying it with a coordinate file that has chain IDs. You could do that, but doing the house-keeping to assign those IDs is tricky, and with PDB you're probably limited by 26 letters. make_ndx will also let you create a group according to a range of atomic numbers a 1-10 or residue numbers r 1-10. This avoids needing to preserve/create chain IDs. Since you only need to create index groups once for a given coordinate file, that's not too onerous. If you will have lots of simulations with different numbers of such groups then you might write a script to automate that... see http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive If your system is N identical peptides in a solvent, then best practice for generating a complete .top is to generate one for a single peptide in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a coordinate file which contains the N peptides' coordinates followed by all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] section of the original .top to match. Other solutions are possible, but require more involved use of pdb2gmx, and might indeed want chain IDs. Uh, thanks. Not sure to have understood all of it, but I will do my homework before coming back :) Sure. Doing some irrelevant tutorial material can be useful introductions to the workflows. Regard;ess, the learning curve can be steep for all computational chemistry software. Unfortunately no beginner these days seems to want to come in and just do protein-in-water :-) That makes their life hard. 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
[gmx-users] unit of eigenfrequency
Hi, After the g_nmeig command the mass weighted eigenfrequency is obtained.So what is the unit of this.I calculated this by GROMACS unit and it came out to be ps-1.If it is this then how to get this in general cm-i unit.Please help me. Abhijit ___ 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] What is best way to get multiple chains?
Mark Abraham ha scritto: ms wrote: Mark Abraham ha scritto: What do you want the chain identifiers for? I'm not aware of a post-pdb2gmx purpose that they might serve. This is where my naivety probably enters in: Analysis programs work on groups. If several chains are defined, can each of these count as a group? Indeed, chapter 8 doesn't explicitly say so, but... My intention is to get analysis for each chain in my system. What is best practice for that / where should I look in the docs? make_ndx is the tool for generating such groups. If you read make_ndx -h you'll see it does indeed let you create groups based around chain IDs, but that'd (at least) require supplying it with a coordinate file that has chain IDs. You could do that, but doing the house-keeping to assign those IDs is tricky, and with PDB you're probably limited by 26 letters. make_ndx will also let you create a group according to a range of atomic numbers a 1-10 or residue numbers r 1-10. This avoids needing to preserve/create chain IDs. Since you only need to create index groups once for a given coordinate file, that's not too onerous. If you will have lots of simulations with different numbers of such groups then you might write a script to automate that... see http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do you mind if I later I try to update the multiple chains wiki page based on your advices? If your system is N identical peptides in a solvent, then best practice for generating a complete .top is to generate one for a single peptide in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a coordinate file which contains the N peptides' coordinates followed by all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] section of the original .top to match. Other solutions are possible, but require more involved use of pdb2gmx, and might indeed want chain IDs. Uh, thanks. Not sure to have understood all of it, but I will do my homework before coming back :) Sure. Doing some irrelevant tutorial material can be useful introductions to the workflows. Regard;ess, the learning curve can be steep for all computational chemistry software. Unfortunately no beginner these days seems to want to come in and just do protein-in-water :-) That makes their life hard. Yep, unfortunately that's kinda not simply protein-in-water. I am trying to understand all pieces I need very slowly, step-by-step. And I guess you will hear my cries often in this ML :) Thanks again, 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] What is best way to get multiple chains?
ms wrote: Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do you mind if I later I try to update the multiple chains wiki page based on your advices? Updates from users who have relevant experience is what continually makes the documentation better! The section on Non-identical chains is not written as clearly as it could be. I'll update it a bit soon, but anything you can add based on your experiences would probably be quite useful as well. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] Re: Advantage of NPT over NVT?
Vitaly V. Chaban wrote: If your model gives a correct fluid density with NPT, use NPT. If it does not, then use NVT. This is a quick practical guide, not not read much. :) Sounds dangerous :-) If the model produces a wrong density, you'd want to be reasonably confident your observable is not linked to the underlying cause, before just proceeding at NVT... Sounds like a really easy criticism for a reviewer to knock back a paper on. Mark, It sounds dangerous if the model is not thoroughly tested. If you know that the model is OK using NVT, but it gives a bit wrong density with NPT - this is an argument to select the first ensemble. Such behaviour is peculiar to a big number of rigid particle models. Vitaly ___ 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: Advantage of NPT over NVT?
Vitaly V. Chaban wrote: Vitaly V. Chaban wrote: If your model gives a correct fluid density with NPT, use NPT. If it does not, then use NVT. This is a quick practical guide, not not read much. :) Sounds dangerous :-) If the model produces a wrong density, you'd want to be reasonably confident your observable is not linked to the underlying cause, before just proceeding at NVT... Sounds like a really easy criticism for a reviewer to knock back a paper on. Mark, It sounds dangerous if the model is not thoroughly tested. If you know that the model is OK using NVT, but it gives a bit wrong density with NPT - this is an argument to select the first ensemble. Such behaviour is peculiar to a big number of rigid particle models. Sure. Having demonstrated it's OK is the important thing. The original context was advice to a newcomer, who might well not appreciate that point. :-) 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
Re: [gmx-users] grompp: no such moleculetype
Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiquitin which is provided on the MARTINI web page. I encountered the same problem as with my protein. I started from files provided in /output.exercises/protein/protein_data/ubiquitin, i.e.: martini_v2.1.itp cg.gro cg.itp cg.top protein-in-vacuum.mdp I commented out all W in cg.top. At the command $ grompp -np 4 -f protein-in-vacuum.mdp -c cg.gro -p cg.top -o cg.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... WARNING 1 [file protein-in-vacuum.mdp, line unknown]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb/rvdw. calling /lib/cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 processing coordinates... Warning: atom names in cg.top and cg.gro don't match (BCQd - BN0) Warning: atom names in cg.top and cg.gro don't match (SCC5 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP4 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC1) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC2) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC3) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC2 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEC3 - SC1) Warning: atom names in cg.top and cg.gro don't match (SEQd - SC2) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) Warning: atom names in cg.top and cg.gro don't match (STAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) (more than 20 non-matching atom names) WARNING 2 [file cg.top, line 22]: 163 non-matching atom names atom names from cg.top will be used atom names from cg.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 160 # G96ANGLES: 161 # PDIHS: 9 # IDIHS: 4 # CONSTR: 30 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 0 OTHER residues There are:76PROTEIN residues There are: 0DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group Non-Protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. = From the name protein-in-vacuum.mdp I assume that there is no HOH around in such file. Also, the tutorial was not for other non-protein. I would be very grateful to the kind person who points out where I did wrongly. Attached is also the mdout.mdp file. thanks francesco pietra On Mon, Oct 5, 2009 at 11:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Look at the .mdp file. You will find Non-Protein somewhere. The .mdp I used is not from a tutorial; it is the general purpose - or standard - mdp provided by Martini. It doe not contain the word protein The protein-in-vacuum.mdp from the ubiquitin CG tutoria does contain both Protein and Non-Protein words. deleting Non-Protein, the error from running grompp is: Fatal error: Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values This comes up because you've defined one group now for T-coupling and assigned coupling constants and temperatures for two. Haphazard changes to .mdp files will certainly generate these errors. Deleting until the problem goes away never works - it only creates more problems :) Please see the manual for proper use of tc-grps, etc. I'll settle the matter until I can generate ideas, or be less tired to check again for the presence of that mysterious non-protein. The real protein contains chloride ion ligands. I have cleared from them before starting with CG and anyway no trace of cl CL Cl. So that has nothing to do with it. Hope to be able to come again here with a solution of this affair. The best advice - don't blindly use some .mdp
Re: [gmx-users] grompp: no such moleculetype
Francesco Pietra wrote: Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiquitin which is provided on the MARTINI web page. I encountered the same problem as with my protein. I started from files provided in /output.exercises/protein/protein_data/ubiquitin, i.e.: martini_v2.1.itp cg.gro cg.itp cg.top protein-in-vacuum.mdp I commented out all W in cg.top. At the command $ grompp -np 4 -f protein-in-vacuum.mdp -c cg.gro -p cg.top -o cg.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... WARNING 1 [file protein-in-vacuum.mdp, line unknown]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb/rvdw. calling /lib/cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 processing coordinates... Warning: atom names in cg.top and cg.gro don't match (BCQd - BN0) Warning: atom names in cg.top and cg.gro don't match (SCC5 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP4 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC1) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC2) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC3) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC2 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEC3 - SC1) Warning: atom names in cg.top and cg.gro don't match (SEQd - SC2) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) Warning: atom names in cg.top and cg.gro don't match (STAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) (more than 20 non-matching atom names) WARNING 2 [file cg.top, line 22]: 163 non-matching atom names atom names from cg.top will be used atom names from cg.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 160 # G96ANGLES: 161 # PDIHS: 9 # IDIHS: 4 # CONSTR: 30 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 0 OTHER residues There are:76PROTEIN residues There are: 0DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group Non-Protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. = From the name protein-in-vacuum.mdp I assume that there is no HOH You know what happens when you assume... around in such file. Also, the tutorial was not for other non-protein. I would be very grateful to the kind person who points out where I did wrongly. Attached is also the mdout.mdp file. Read the .mdp file you're using. There are two very clear appearances of the Non-Protein term (energygrps and tc-grps). Don't simply trust an .mdp file you found somewhere and are potentially having to hack at. Read the input, determine the appropriate settings and why those you're using may not work. -Justin thanks francesco pietra On Mon, Oct 5, 2009 at 11:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Look at the .mdp file. You will find Non-Protein somewhere. The .mdp I used is not from a tutorial; it is the general purpose - or standard - mdp provided by Martini. It doe not contain the word protein The protein-in-vacuum.mdp from the ubiquitin CG tutoria does contain both Protein and Non-Protein words. deleting Non-Protein, the error from running grompp is: Fatal error: Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values This comes up because you've defined one group now for T-coupling and assigned coupling constants and temperatures for two. Haphazard changes to .mdp files will certainly generate these errors. Deleting until the problem goes away never works - it only creates more problems :) Please see the manual for proper use of tc-grps, etc. I'll settle the matter until I can
Re: [gmx-users] grompp: no such moleculetype
On Wed, Oct 14, 2009 at 7:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiquitin which is provided on the MARTINI web page. I encountered the same problem as with my protein. I started from files provided in /output.exercises/protein/protein_data/ubiquitin, i.e.: martini_v2.1.itp cg.gro cg.itp cg.top protein-in-vacuum.mdp I commented out all W in cg.top. At the command $ grompp -np 4 -f protein-in-vacuum.mdp -c cg.gro -p cg.top -o cg.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... WARNING 1 [file protein-in-vacuum.mdp, line unknown]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb/rvdw. calling /lib/cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 processing coordinates... Warning: atom names in cg.top and cg.gro don't match (BCQd - BN0) Warning: atom names in cg.top and cg.gro don't match (SCC5 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP4 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC1) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC2) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC3) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC2 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEC3 - SC1) Warning: atom names in cg.top and cg.gro don't match (SEQd - SC2) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) Warning: atom names in cg.top and cg.gro don't match (STAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) (more than 20 non-matching atom names) WARNING 2 [file cg.top, line 22]: 163 non-matching atom names atom names from cg.top will be used atom names from cg.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 160 # G96ANGLES: 161 # PDIHS: 9 # IDIHS: 4 # CONSTR: 30 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 0 OTHER residues There are: 76 PROTEIN residues There are: 0 DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group Non-Protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. = From the name protein-in-vacuum.mdp I assume that there is no HOH You know what happens when you assume... around in such file. Also, the tutorial was not for other non-protein. I would be very grateful to the kind person who points out where I did wrongly. Attached is also the mdout.mdp file. Read the .mdp file you're using. There are two very clear appearances of the Non-Protein term (energygrps and tc-grps). Don't simply trust an .mdp file you found somewhere was not found somewhere. It is the file provided by the author of that tutorial right for that tutorial (everything was taken from the solution provided to the example). and are potentially having to hack at. Read the input, determine the appropriate settings and why those you're using may not work. I'll look at. But I fear that by commenting out what alludes to non-protein (if this is what I should do; if not, please explain what I should do), it will not work. It was so with my protein. At any event, for a person like me coming from AMBER, it is surprising that there is no minimum input that works with every standard protein. Thanks francesco -Justin thanks francesco pietra On Mon, Oct 5, 2009 at 11:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Look at the .mdp file. You will find Non-Protein somewhere. The .mdp I used is not from a tutorial; it is the general purpose - or standard - mdp
Re: [gmx-users] grompp: no such moleculetype
Francesco Pietra wrote: On Wed, Oct 14, 2009 at 7:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiquitin which is provided on the MARTINI web page. I encountered the same problem as with my protein. I started from files provided in /output.exercises/protein/protein_data/ubiquitin, i.e.: martini_v2.1.itp cg.gro cg.itp cg.top protein-in-vacuum.mdp I commented out all W in cg.top. At the command $ grompp -np 4 -f protein-in-vacuum.mdp -c cg.gro -p cg.top -o cg.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... WARNING 1 [file protein-in-vacuum.mdp, line unknown]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb/rvdw. calling /lib/cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 processing coordinates... Warning: atom names in cg.top and cg.gro don't match (BCQd - BN0) Warning: atom names in cg.top and cg.gro don't match (SCC5 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP4 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC1) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC2) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC3) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC2 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEC3 - SC1) Warning: atom names in cg.top and cg.gro don't match (SEQd - SC2) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) Warning: atom names in cg.top and cg.gro don't match (STAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) (more than 20 non-matching atom names) WARNING 2 [file cg.top, line 22]: 163 non-matching atom names atom names from cg.top will be used atom names from cg.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 160 # G96ANGLES: 161 # PDIHS: 9 # IDIHS: 4 # CONSTR: 30 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 0 OTHER residues There are:76PROTEIN residues There are: 0DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group Non-Protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. = From the name protein-in-vacuum.mdp I assume that there is no HOH You know what happens when you assume... around in such file. Also, the tutorial was not for other non-protein. I would be very grateful to the kind person who points out where I did wrongly. Attached is also the mdout.mdp file. Read the .mdp file you're using. There are two very clear appearances of the Non-Protein term (energygrps and tc-grps). Don't simply trust an .mdp file you found somewhere was not found somewhere. It is the file provided by the author of that tutorial right for that tutorial (everything was taken from the solution provided to the example). Indeed, it may work in certain cases, but my general advice is simply this: if you didn't make it yourself with manual in hand, you have to still comb through it to make sure it addresses your system. If you have only protein, and Non-Protein is defined somewhere, then the .mdp file does not suit your needs. I have also seen many instances of files that work in tutorials (topologies, scripts, .mdp files) wind up not working when I look into them. This is not to say that any particular individual has posted anything incorrectly, but always check your input for yourself! and are potentially having to hack at. Read the input, determine the appropriate settings and why those you're using may not work. I'll look at. But I fear that by commenting out what alludes to non-protein (if this is what I should do; if
[gmx-users] question about all atoms lipid molecule structure and force field
Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar with any such work ? Is there any all atom model for hydrocarbons which is incorporated in Gromacs? I am not 100 % sure about it. I want to do this to parametrize another force field which essentially uses all atom model. Thank you, Amit ___ 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: Re: [gmx-users] RMSF reference state?
Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this?With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -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] weird tabulated potential problem
Hi, Some months ago I reported a strange conflict between the GMX 4 new option nblist=-1 and tabulated potentials. At that time I contacted Berk and he could run my test system without any problem. So I thought I had something wrong for my system configurations. However, recently I re-checked the problem and found I got similar issues from two different software/hardware configurations. It seems the problem is sort of general. I'm wondering if any developer or people who are familiar with the code can help me to figure out the problem. The problem is like the follows. When I use nblist=-1 option with tabulated nonbond interation, sometimes I got a segmatation fault. I used nonebond tables with space 0.004 nm and I smoothed the curves so no complain of wrong numerical derivatives from GMX were found. I tested the simulation on three machines: A: Intel i7 gcc 4.1.2 B: Intel Xeon icc 10.1 C: AMD Barcelona icc 10.1 All tests were done using one CPU core. It seems system A/B always gave me troubles and C was fine. I first used rlist =1.3 and rvdw=1.2 to give a 0.1 buffer. And I found the potential energys from A/B were weired with values sometimes as 1.0e29. And the potential energy with C is always around 1.0e3. When I set rlist=1.28, I can optimize the Average neighborlist lifetime about 11, as Berk onece suggested. But in this buffer size, simulations with A/B got segmentation fault immediately. Interestingly, I tried to try many conventional force field simulations/CG simulations with tabulated potentials before with A/B, and all of them seemed to be fine if I didn't use nblist=-1 with tabulated potentials. Can anyone give me any suggestions? Thanks, Lanyuan _ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TLswm=1___ 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] question about all atoms lipid molecule structure and force field
Hi, You can find some configurations here: http://persweb.wabash.edu/facstaff/fellers/ And I think you can use Charmm FF. Lanyuan Date: Wed, 14 Oct 2009 11:29:26 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about all atoms lipid molecule structure and force field Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar with any such work ? Is there any all atom model for hydrocarbons which is incorporated in Gromacs? I am not 100 % sure about it. I want to do this to parametrize another force field which essentially uses all atom model. Thank you,Amit _ MSN十周年庆典，查看MSN注册时间，赢取神秘大奖 http://10.msn.com.cn___ 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: Re: [gmx-users] RMSF reference state?
Hi Pan Wu, There are two things to distinguish: 1. The reference structure used to remove translational and rotational degrees of freedom 2. The reference against which the deviations (on a per atom base) are calculated that are then squared, averaged and taken the root of (root mean square fluctuation). These two need not be the same. It is common, and most sensible, to calculate the deviations against the average structure, after fitting all structures in the trajectory against a certain reference structure. With option -od the deviations against the reference used for fitting are calculated rather than against the average. You do need a reference for fitting, since otherwise you include overall rotation and translation in the calculation of the RMSF, which you usually wouldn't want. I hope this makes it clear. Cheers, Tsjerk On Wed, Oct 14, 2009 at 9:12 PM, Pan Wu pan...@duke.edu wrote: Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -Justin ___ 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. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://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] RMSF reference state?
Pan Wu wrote: Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? You're talking about two separate calculations. Using -od calculates some sort of RMSD. If you do not use -od, then the standard output (-o) is RMSF, using the fitting described (unless you use -nofit). -Justin Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] RMSF reference state?
Hi, Actually, Justin is completely right (and I should've checked g_rmsf -h). -od calculates the RMSD from the structure in the frame against the structure in the topology file. This does not nullify the statements regarding references for fitting and references for deviations though :p Cheers, Tsjerk On Wed, Oct 14, 2009 at 9:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Pan Wu wrote: Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? You're talking about two separate calculations. Using -od calculates some sort of RMSD. If you do not use -od, then the standard output (-o) is RMSF, using the fitting described (unless you use -nofit). -Justin Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -Justin ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 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. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://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] simulation end with Segmentation fault, error message said something about libSystem.B.dylib
Hi, Lately few of my simulations had ended up with wired output: Writing final coordinates. step 50, remaining runtime: 0 s [xn068:94365] *** Process received signal *** [xn068:94365] Signal: Segmentation fault (11) [xn068:94365] Signal code: Address not mapped (1) [xn068:94365] Failing at address: 0x108ee9000 [xn068:94365] [ 0] 2 libSystem.B.dylib 0x844e83fa _sigtramp + 26 [xn068:94365] [ 1] 3 ??? 0x00801b78 0x0 + 8395640 [xn068:94365] *** End of error message *** In addition, the output files are not usable. We use apple with 10.5 (server version) and gromacs (4.0.5) is compiles using 64bit. Any idea someone? Best, Itamar ___ 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] simulation end with Segmentation fault, error message said something about libSystem.B.dylib
Itamar Kass wrote: Hi, Lately few of my simulations had ended up with wired output: Writing final coordinates. step 50, remaining runtime: 0 s [xn068:94365] *** Process received signal *** [xn068:94365] Signal: Segmentation fault (11) [xn068:94365] Signal code: Address not mapped (1) [xn068:94365] Failing at address: 0x108ee9000 [xn068:94365] [ 0] 2 libSystem.B.dylib 0x844e83fa _sigtramp + 26 [xn068:94365] [ 1] 3 ??? 0x00801b78 0x0 + 8395640 [xn068:94365] *** End of error message *** In addition, the output files are not usable. We use apple with 10.5 (server version) and gromacs (4.0.5) is compiles using 64bit. Any idea someone? What was the command line? What's the end of the .log file? What filesystem are you using? Did it fill? 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
Re: [gmx-users] question about all atoms lipid molecule structure and force field
Thank you, Is it really necessary for me to use Charmm FF for all atom calculations on lipids? The reason I am asking this is because it will require me to create gromacs compatible FF files of the Charmm FF . I did find two perl scripts which can do probably handle that but i am wondering if the compatible FF are already up on gromacs website somewhere. amit 2009/10/14 LuLanyuan lulany...@msn.com Hi, You can find some configurations here: http://persweb.wabash.edu/facstaff/fellers/ And I think you can use Charmm FF. Lanyuan -- Date: Wed, 14 Oct 2009 11:29:26 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about all atoms lipid molecule structure and force field Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar with any such work ? Is there any all atom model for hydrocarbons which is incorporated in Gromacs? I am not 100 % sure about it. I want to do this to parametrize another force field which essentially uses all atom model. Thank you, Amit -- Messenger保护盾2.0，更安全可靠的Messenger聊天！ 现在就下载！ http://im.live.cn/safe/ ___ 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] question about all atoms lipid molecule structure and force field
Amit Choubey wrote: Thank you, Is it really necessary for me to use Charmm FF for all atom calculations on lipids? You can use whatever model you want, provided it's valid. Just so happens that most people who use all-atom models of lipids use CHARMM. The reason I am asking this is because it will require me to create gromacs compatible FF files of the Charmm FF . I did find two perl scripts which can do probably handle that but i am wondering if the compatible FF are already up on gromacs website somewhere. No one ever said life was easy :) CHARMM support is under development, you can get the source via the git repositories, but I don't know its current status. -Justin amit 2009/10/14 LuLanyuan lulany...@msn.com mailto:lulany...@msn.com Hi, You can find some configurations here: http://persweb.wabash.edu/facstaff/fellers/ And I think you can use Charmm FF. Lanyuan Date: Wed, 14 Oct 2009 11:29:26 -0700 From: kgp.a...@gmail.com mailto:kgp.a...@gmail.com To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: [gmx-users] question about all atoms lipid molecule structure and force field Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar with any such work ? Is there any all atom model for hydrocarbons which is incorporated in Gromacs? I am not 100 % sure about it. I want to do this to parametrize another force field which essentially uses all atom model. Thank you, Amit Messenger保护盾2.0，更安全可靠的Messenger聊天！ 现在就下载！ http://im.live.cn/safe/ ___ 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 ___ 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 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] Fwd: unit of eigenfrequency
Hi, After the g_nmeig command the mass weighted eigenfrequency is obtained.So what is the unit of this.I calculated this by GROMACS unit and it came out to be ps-1.If it is this then how to get this in general cm-i unit.Please help me. Abhijit ___ 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] simulation end with Segmentation fault, error message said something about libSystem.B.dylib
On Thu, Oct 15, 2009 at 1:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Itamar Kass wrote: Hi, Lately few of my simulations had ended up with wired output: Writing final coordinates. step 50, remaining runtime: 0 s [xn068:94365] *** Process received signal *** [xn068:94365] Signal: Segmentation fault (11) [xn068:94365] Signal code: Address not mapped (1) [xn068:94365] Failing at address: 0x108ee9000 [xn068:94365] [ 0] 2 libSystem.B.dylib 0x844e83fa _sigtramp + 26 [xn068:94365] [ 1] 3 ??? 0x00801b78 0x0 + 8395640 [xn068:94365] *** End of error message *** In addition, the output files are not usable. We use apple with 10.5 (server version) and gromacs (4.0.5) is compiles using 64bit. Any idea someone? What was the command line? mpiexec mdrun_mpi -pd -s one_GroEL_noATP_run2_for_MD6.tpr -o one_GroEL_noATP_run2_from_MD6.trr -c one_GroEL_noATP_run2_from_MD6.gro -e one_GroEL_noATP_run2 _from_MD6.edr -x one_GroEL_noATP_run2_from_MD6.xtc -g one_GroEL_noATP_run2_from_MD6.log -v -stepout 5000 I am using -pd 'cause I am using SHAKE. What's the end of the .log file? I gave the mdrun output and not the logfile 'cause there is nothing speaciel there. It write the temp, energy etc. which look OK and then stop: Step Time Lambda 499800 999.60.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.05518e+033.39568e+032.06800e+03 -2.23433e+028.39937e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.54232e+05 -2.10739e+04 -3.24147e+06 -3.58373e+04 -6.38806e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -2.80974e+064.96949e+05 -2.31279e+063.05107e+02 -3.18227e+01 Step Time Lambda 499900 999.80.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.09295e+033.38158e+032.12674e+03 -1.83503e+028.36385e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.54228e+05 -2.10769e+04 -3.24015e+06 -3.55380e+04 -6.38776e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -2.80836e+064.95856e+05 -2.31250e+063.04437e+02 -1.27131e+01 Step Time Lambda 50 1000.00.0 Writing checkpoint, step 50 at Wed Oct 14 17:34:47 2009 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.53869e+033.32588e+032.03245e+03 -2.36432e+028.41339e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.57725e+05 -2.10767e+04 -3.24340e+06 -3.52958e+04 -6.38808e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -2.80813e+064.96000e+05 -2.31213e+063.04525e+029.63155e+01 What filesystem are you using? We are using MAC so this is Mac OS Extended (Journaled). Did it fill? 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 ___ 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
