Re: [gmx-users] Coordinate file for lipid bilayer
Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James 2012/5/26 Peter C. Lai p...@uab.edu Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0 Tieleman's lipids require you to generate a dummy tpr for use with trjconv to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro -pbc mol -ur compact) first. Lots of people have their own bilayer but they may be for different FFs which means the atom naming would not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC or POPE bilayer using Tieleman's parameters for lipids by means of gromos united atom force field. The main problem is that the pre-equilibrated bilayers wich I found on the Dr. Tieleman's site consist of no more that 128 lipids but I want to simulate my protein with bigger number of lipids ( for example starting from 200 lipids ). What should I do in that case ? Could you provide me with some tools for construction of such united-atoms bilayers with desired dimensions ? Finally is there any others pre-equilibrated bilayers aviable for downloading besides Dr. Tieleman's site ? thanks for your help, James S. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
Hi, The easiest solution is probably to write a script that reorders the structure file (gro for example, just swap the lines in each lipid, and use editconf -f file.gro -resnr 1 to renumber) the way it is written in the topology. Cheers Jon On 2012-05-28 08:03, James Starlight wrote: Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James 2012/5/26 Peter C. Lai p...@uab.edu mailto:p...@uab.edu Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0 Tieleman's lipids require you to generate a dummy tpr for use with trjconv to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro -pbc mol -ur compact) first. Lots of people have their own bilayer but they may be for different FFs which means the atom naming would not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC or POPE bilayer using Tieleman's parameters for lipids by means of gromos united atom force field. The main problem is that the pre-equilibrated bilayers wich I found on the Dr. Tieleman's site consist of no more that 128 lipids but I want to simulate my protein with bigger number of lipids ( for example starting from 200 lipids ). What should I do in that case ? Could you provide me with some tools for construction of such united-atoms bilayers with desired dimensions ? Finally is there any others pre-equilibrated bilayers aviable for downloading besides Dr. Tieleman's site ? thanks for your help, James S. -- gmx-users mailing list 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- _ Jon Kapla Division of Physical Chemistry Dpt. of Materials and Environmental Chemistry (MMK) Arrhenius Laboratory Stockholm University SE-106 91 Stockholm Pos:PhD Student Phone: +46 8 16 11 79 (office) Phone: +46 70 304 19 89 (cell) E-mail: jon.ka...@mmk.su.se _ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Extend Umbrella Windows
Dear Justin and Gmx users, I want to extend my simulation in each window of 20 ns. For this purpose I should use (example - window 0): tpbconv -s umbrella0.tpr -extend 2 -o umbrella0extend.tpr mdrun -s umbrella0extend.tpr -cpi umbrella0.cpt -deffnm umbrella0 -pf pullf0.xvg -px pullx0.xvg My questions: 1. Do I have to use -deffnm , -px, -pf or without this my files will be updated to the one produced before? 2. Will the umbrella0extend.tpr shall be used for a g_wham or my previous umbrella0.tpr combined with umbrella0extend.tpr? How to combine them? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] crude interaction energy using g_energy
I think the reality of biological systems is represented as such accurately. Everyone always strives in biochemistry for a precise number, ie binding affinity = 489.489 exactly. In real systems there are to many variables (solvent, ions, particular position of moving amino acids at point A or B, etc...). The original rule of thumb for beginning to study these systems was to do 100 MD simulations, but I personally think a small sample space will give you the same exact mean and STD deviation, STD error, etc... (ie 10-20 runs). There is, as larger MD's are now becoming more common still no set standard for this. A quick way, which also generates the same variability but is faster (if you dont want a nice curve and just the end mean value) is to do MD A at the bound position and EQ it for a couple nano seconds using NV P and T, and then state B unbound the same, then 20 runs is manageable time wise, but you get no pretty curves, ie no transition states which are of interest in many cases, such as particular amino acids, or conformational changes which include several states. I think this might help, although some analysis tools for large scale biological systems (ie say pulling contributions energy wise for a particular amino acid) would be an asset...as I have found none that dont require pulling energies, etc...alot of work at the moment. Stephan Watkins Univerity of Bern Original-Nachricht Datum: Sun, 27 May 2012 20:44:48 -0400 Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] crude interaction energy using g_energy On 5/27/12 8:41 PM, sai nitin wrote: Dear all, Recently i performed two 15ns simulation of protein-ligand systems using gromacs of my interest...and using g_energy tool..i calculated crude interaction energy based on short-‐range energy components Eint = ELJ + ECoul. ...I got two Eints for two simulations 1) Eint = -51.003 Kcal/mol (first simulation) 2) Eint = -26.615 Kcal/mol (second simulation) Can anybody tell me what meaning can i make out of it...means is first simulation is more stable than second one..or vice versa... I don't think you can say anything about stability based on these figures. In simulation 1, the interaction is more stable than in simulation 2. It seems clear that the two simulations behaved somewhat differently, but the exact differences will only become apparent through other analyses and visualization. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Fwd: amber2xtc.py error
hello: I am trying to use amber2xtc.py script to convert Amber MD system into gromacs format by command: python amber2xtc.py npt3.mdcrd apo.prmtop . *.rst md_gromacs however, I got the following messages --log USAGE : python amber2xtc.py AMBERCRD AMBERTOP TRAJDIR TRAJPATTERN OUTPUTPREFIX Example : python amber2xtc.py mdcrd.crd mdcrd.top md *.x.gz md_gromacs Note that the AmberCrd can also be a PDB file. Will convert the following files : ['m1.rst'] currently converting m1.rst ls: cannot access *.pdb.*: No such file or directory -- I am wondering how to fix this problem? thank you very much A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Umbrella Profile
On Fri, May 18, 2012 at 1:27 PM, Steven Neumann s.neuman...@gmail.comwrote: On Fri, May 18, 2012 at 12:22 PM, Justin A. Lemkul jalem...@vt.eduwrote: I have no idea why you observe the dip, but it's probably irrelevant as you don't need a reaction coordinate that long, if this is the same plot that we've been discussing on the list. I must ask that you always post to the mailing list, for your own benefit, especially in the immediate future as I will be traveling for some time and will not reply very quickly to email; you stand a better chance getting help from others. I am also generally unable to dedicate much time debugging others' research on a personal level. -Justin Thank you Justin. I decreased the reaction coordinate and this dip still occurs: http://speedy.sh/2qHNa/Profile2.JPG Its because of the applied weight of WHAM. Any suggestions please? Steven Hi Justin, I run umbrella sampling of my ligand binding to different part of my residues. Each time my PMF profile is smooth but at the end the small dip occurs. Here another example: http://speedy.sh/dbUg9/ProfileHA1.JPG http://speedy.sh/8zZ52/HistoHA1.JPG What can be causing this? Shall I just igonore this taking the plateau value or run a longer simulations in each window? Best, Steven On 5/18/12 4:17 AM, Steven Neumann wrote: Dear Justin, I run umbrella sampling (pulling ligand away from the protein) simulations to get deltaG: http://speedy.sh/XpUks/**Profile.JPGhttp://speedy.sh/XpUks/Profile.JPG http://speedy.sh/yvJKx/**Histogram.JPGhttp://speedy.sh/yvJKx/Histogram.JPG I know I need one more window around 1 nm but apart from this histrogram looks really good. My each window was 50 ns. Why the plateau in the end goes down of 0.4 kcal/mol? Would you suggest longer simulation in each window? Thank you and sorry for writing straight to your email, Best Steven -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Extend Umbrella Windows
On 5/28/12 5:45 AM, Steven Neumann wrote: Dear Justin and Gmx users, I want to extend my simulation in each window of 20 ns. For this purpose I should use (example - window 0): tpbconv -s umbrella0.tpr -extend 2 -o umbrella0extend.tpr mdrun -s umbrella0extend.tpr -cpi umbrella0.cpt -deffnm umbrella0 -pf pullf0.xvg -px pullx0.xvg My questions: 1. Do I have to use -deffnm , -px, -pf or without this my files will be updated to the one produced before? Assuming you are using the latest version of Gromacs, -append is default and as such the file names recorded in the .cpt file should be used. 2. Will the umbrella0extend.tpr shall be used for a g_wham or my previous umbrella0.tpr combined with umbrella0extend.tpr? How to combine them? It may or may not matter which you use, since the information pertaining to the umbrella sampling itself is not different. You can't combine .tpr files; there's no need to. In your case, umbrella0.tpr contains information for the first time interval and umbrella0extend.tpr contains that same interval plus 20 ns. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] comparing simulations with diffrent forcefields
On 5/28/12 7:07 AM, Kowsar Bagherzadeh wrote: Dear users, I have done a Ligand-Protein Simulation using 43a1.ff forcefield and ssDNA-Protein (the same protein I used for ligand protein simulation) using amber99sd-ILDN forcefield. Is it possible to compare the results of the two simulation with eachother? No? Maybe it's possible, but there will be a lot of caveats to the results. You may know of some intrinsic limitations or benefits of each force field that may explain away discrepancies, but the real complication comes with the ligand. How did you generate its parameters? Do you know exactly how those parameters will affect the local dynamics of the residues in which it makes contact? Do you know the equivalent result using a suitable Amber force field? If the answer to any of these questions is no, you'll have a hard time convincing a reviewer that your comparison is very meaningful. Net result: choose a force field, and use it for all simulations you wish to compare. It is substantially easier than trying to wiggle your way into a potentially incomplete or incorrect interpretation of the results. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Coordinate file for lipid bilayer
Sounds dangerous to me. Here's a possible methods section from your paper: we obtained a popc bilayer somewhere on the internet. Unfortunately, this structure did not match our topology file. Nevertheless, it has the same number of atoms and so we assumed that the difference was simply a matter of reordering ... (not too appealing I think). Peter's advice was good and I recommend avoiding a reordering based on an assumption that it will be correct. Using the method that Peter outlined, there will be some issues with equilibration at the new periodic boundary, but 100 ns of MD simulation should take care of that just fine (note that the Tieleman 128 lipid file is pretty old and, computers being slower then, I imagine that it was equilibrated with fewer than 100 ns itself). Chris. On 2012-05-28 08:03, James Starlight wrote: Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Position Restraints of one of the moleculetpye
Dear Gmx Users, I am fighting with the position restraints. My system cosnsists of 6 ligands - all of them have the same topology - ligand.itp. I want to: 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre ligand1.itp 2. Restrain 5 of them and pull one of them away. Here I came across some difficulties. I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp and by index files I create an index of the ligands I wan to restrain. Each my ligands has 46 atoms. When I process to grompp: Atom index (256) in position_restraints out of bounds (1-46). This probably means that you have inserted topology section position_restraints Shall I rename Ligands as different residue names? If my posre includes 1-46 atom all ligands are restraints? How to restrain just 5 out of 6 of them? Best, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] no pr.gro file for energy minimization
Hello After equilibrating the water around my molecule I want to run the MD simulation. In my tutorial this is primed with: grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr I don't have this pr.gro file but I have a pr.tpr file. Could I use this one? It seems GROMACS accepts this but I don't know whether this is good. I have this pr.tpr file because I used in the equilibrating the water procedure the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] no pr.gro file for energy minimization
A question: why do you not have a pr.gro? It should been output by the mdrun of pr.tpr? Anyway, yes you should be able to use -c pr.tpr. However you need to make sure to use -t pr.trr or -t pr.cpt to ensure it uses the coordinates and velocities from the end of the equilibration run. Even if you use -c pr.gro, it is a good idea to use -t to ensure that it uses the full-precision coordinates and velocities from the previous run. The -c .gro/.tpr are at a minimum necessary for grompp to put atom names into the new .tpr file that it generates. On 2012-05-28 04:21:35PM +0100, Lara Bunte wrote: Hello After equilibrating the water around my molecule I want to run the MD simulation. In my tutorial this is primed with: grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr I don't have this pr.gro file but I have a pr.tpr file. Could I use this one? It seems GROMACS accepts this but I don't know whether this is good. I have this pr.tpr file because I used in the equilibrating the water procedure the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Position Restraints of one of the moleculetpye
On 5/28/12 10:48 AM, Steven Neumann wrote: Dear Gmx Users, I am fighting with the position restraints. My system cosnsists of 6 ligands - all of them have the same topology - ligand.itp. I want to: 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre ligand1.itp 2. Restrain 5 of them and pull one of them away. Here I came across some difficulties. I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp and by index files I create an index of the ligands I wan to restrain. Each my ligands has 46 atoms. When I process to grompp: Atom index (256) in position_restraints out of bounds (1-46). This probably means that you have inserted topology section position_restraints Shall I rename Ligands as different residue names? If my posre includes 1-46 atom all ligands are restraints? How to restrain just 5 out of 6 of them? Position restraints are applied on a per-moleculetype basis. If you have six copies of a ligand, the only way to do this is to define the sixth as a special [moleculetype] (even if it contains identical information) with a different name, such that it can be restrained in the absence of restraints on the others. See the logic here: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Measure of density in homo- and heterogeneous systems
Dear Gromacs users! In this task I have two systems: First system consist of single layer of Ccl4 molecules. Second system consist of membrane-mimicking layer of Ccl4 surrounded by water and the protein embedded in that biphastic layer. I'd like to measure density in both of my systems to check of its packing degree. How could I do it in the case of homo system- (where I'd like to check density in the Ccl4 layer only) as well as in more complex hetero system ( where I'd like to check density in each layer separately as well as compute averaged density among all layers) ? Thanks for advises, James S. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Measure of density in homo- and heterogeneous systems
On 5/28/12 3:09 PM, James Starlight wrote: Dear Gromacs users! In this task I have two systems: First system consist of single layer of Ccl4 molecules. Second system consist of membrane-mimicking layer of Ccl4 surrounded by water and the protein embedded in that biphastic layer. I'd like to measure density in both of my systems to check of its packing degree. How could I do it in the case of homo system- (where I'd like to check density in the Ccl4 layer only) as well as in more complex hetero system ( where I'd like to check density in each layer separately as well as compute averaged density among all layers) ? The density of the homogeneous system can easily be obtained from the .edr file, as long as the ensemble was NPT. With NVT, the density term is not written, IIRC. In the case of the heterogeneous system, use g_density to obtain partial densities as a function of box dimension. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
Thank you Thomas and Justin for your valuable suggestion. Thomas and Justin, my Query is as follow.. In step six ..We are doing NPT equilibration followed by production run The mdp files for both is same(Except the time of run and saving of output) So why the two mdp are same? Why we not restrain total protein for NPT equilibration (-DPOSRES) and then only POSRES_B (Position restrain on B chain, remove position restrain from other chain) for production run..(these we follow generally)??? The main reason of confusion to me is the same mdp file in Equilibration(npt_umbrella.mdp ) and production run (md_umbrella.mdp). So what is the difference between the NPT equilibration and production run.??? As per Thomas explanation I interpret the following Answer to my Queries.. Please tell me these are right or wrong *So if you want to calculate some equilibrium property of a protein in water you do first a preperation simulation to equilibrate the system (NVE, NVT or NPT - depending for what ensemble you want the property).Normally during this you put position restraints to the protein backbone, so that the protein structure does not gets disturbed during the part where you equilibrate the water. but if your protein is fairly stable / rigid, you don't need these restraints.* So as the protein is stable thats why we are not using the position restrained in NPT.. That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same. Please accept my apology if I interpret any wrong and if unable to explain you my query.. Thanks to Justin and Thomas for there valuable guidance I will be a very greatfull to you if you help me to solve my simple query.. Thank you in advance... With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
Thank you Thomas and Justin for your valuable suggestion. Thomas and Justin, my Query is as follow.. In step six ..We are doing NPT equilibration followed by production run The mdp files for both is same(Except the time of run and saving of output) So why the two mdp are same? Why we not restrain total protein for NPT equilibration (-DPOSRES) and then only POSRES_B (Position restrain on B chain, remove position restrain from other chain) for production run..(these we follow generally)??? The main reason of confusion to me is the same mdp file in Equilibration(npt_umbrella.mdp ) and production run (md_umbrella.mdp). So what is the difference between the NPT equilibration and production run.??? As per Thomas explanation I interpret the following Answer to my Queries.. Please tell me these are right or wrong * So if you want to calculate some equilibrium property of a protein in water you do first a preperation simulation to equilibrate the system (NVE, NVT or NPT - depending for what ensemble you want the property).Normally during this you put position restraints to the protein backbone, so that the protein structure does not gets disturbed during the part where you equilibrate the water. but if your protein is fairly stable / rigid, you don't need these restraints.(Thomas Explanation) * my Interpretation is as follow So as the protein is stable thats why we are not using the position restrained in NPT.. That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same. Please accept my apology if I interpret any wrong and if unable to explain you my query.. Thanks to Justin and Thomas for there valuable guidance I will be a very greatfull to you if you help me to solve my simple query.. Thank you in advance... With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
On 5/28/12 3:12 PM, rama david wrote: Thank you Thomas and Justin for your valuable suggestion. Thomas and Justin, my Query is as follow.. In step six ..We are doing NPT equilibration followed by production run The mdp files for both is same(Except the time of run and saving of output) So why the two mdp are same? Why we not restrain total protein for NPT equilibration (-DPOSRES) and then only POSRES_B (Position restrain on B chain, remove position restrain from other chain) for production run..(these we follow generally)??? The main reason of confusion to me is the same mdp file in Equilibration(npt_umbrella.mdp ) and production run (md_umbrella.mdp). So what is the difference between the NPT equilibration and production run.??? If one were to run an umbrella sampling simulation in each window without prior equilibration, you would normally discard the first few ns as equilibration. All the tutorial is telling you to do is to run some equilibration as a separate step. You can approach the equilibration however you like. As per Thomas explanation I interpret the following Answer to my Queries.. Please tell me these are right or wrong */So if you want to calculate some equilibrium property of a protein in water you do first a preperation simulation to equilibrate the system (NVE, NVT or NPT - depending for what ensemble you want the property).Normally during this you put position restraints to the protein backbone, so that the protein structure does not gets disturbed during the part where you equilibrate the water. but if your protein is fairly stable / rigid, you don't need these restraints./* So as the protein is stable thats why we are not using the position restrained in NPT.. That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same. More or less. The special case with what you're doing in the tutorial is that you have no initiating velocities in each window; you only have coordinates. That's why it makes sense to do a bit of equilibration in each window first, generating velocities and re-equilibrating the system. -Justin Please accept my apology if I interpret any wrong and if unable to explain you my query.. Thanks to Justin and Thomas for there valuable guidance I will be a very greatfull to you if you help me to solve my simple query.. Thank you in advance... With Best Wishes, Rama David. -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
Thank you Justin for reply... More or less. The special case with what you're doing in the tutorial is that you have no initiating velocities in each window; you only have coordinates. That's why it makes sense to do a bit of equilibration in each window first, generating velocities and re-equilibrating the system. -Justin In npt_umbrella.mdp we have gen_vel = yes The command line in tutorial is grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr ... grompp -f npt_umbrella.mdp -c conf450.gro -p topol.top -n index.ndx -o npt22.tpr So if I modify the process as follow, Then is the need of equilibration (Can we skip equilibration and run production md) use -t flag with cpt ( to give velocity of the previous run ) file continuation = yes gen_vel = no . Is these alternative process is right or totally wrong..??? Please give me a valuable suggestion. Thank you in advance. With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
On 5/28/12 3:49 PM, rama david wrote: Thank you Justin for reply... More or less. The special case with what you're doing in the tutorial is that you have no initiating velocities in each window; you only have coordinates. That's why it makes sense to do a bit of equilibration in each window first, generating velocities and re-equilibrating the system. -Justin In npt_umbrella.mdp we have gen_vel = yes The command line in tutorial is grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr ... grompp -f npt_umbrella.mdp -c conf450.gro -p topol.top -n index.ndx -o npt22.tpr So if I modify the process as follow, Then is the need of equilibration (Can we skip equilibration and run production md) use -t flag with cpt ( to give velocity of the previous run ) file continuation = yes gen_vel = no . Is these alternative process is right or totally wrong..??? Using the checkpoint in this instance is wrong. The only checkpoint you have accessible to you at that point is from the end of the pulling simulation and corresponds to the final state of the system. Applying these velocities to the intermediate configurations along the reaction coordinate is likely to do weird and unreliable things to the trajectory. It is more robust to run NPT and then data collection, or as I said before, proceed immediately to a continuous data collection (with gen_vel = yes!) and discard the initial few ns of data as equilibration. In theory, this procedure is no different than any other simulation that one conducts. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
Thank you Justin.. Is these alternative process is right or totally wrong..??? Using the checkpoint in this instance is wrong. The only checkpoint you have accessible to you at that point is from the end of the pulling simulation and corresponds to the final state of the system. Applying these velocities to the intermediate configurations along the reaction coordinate is likely to do weird and unreliable things to the trajectory. It is more robust to run NPT and then data collection, or as I said before, proceed immediately to a continuous data collection (with gen_vel = yes!) and discard the initial few ns of data as equilibration. In theory, this procedure is no different than any other simulation that one conducts. Check point file has velocity of the last co-ordinates and we are using middle configuration.. Thank you for explaination ... I have another query.. In npt equilibration can I use define = -DPOSRES (Position restrain all the protein along the chain B) and in production md define = -DPOSRES_B ( Position restrain for chain B only..) ??? If not What is appropriate reason??? Thank you in advance... With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
On 5/28/12 4:09 PM, rama david wrote: Thank you Justin.. Is these alternative process is right or totally wrong..??? Using the checkpoint in this instance is wrong. The only checkpoint you have accessible to you at that point is from the end of the pulling simulation and corresponds to the final state of the system. Applying these velocities to the intermediate configurations along the reaction coordinate is likely to do weird and unreliable things to the trajectory. It is more robust to run NPT and then data collection, or as I said before, proceed immediately to a continuous data collection (with gen_vel = yes!) and discard the initial few ns of data as equilibration. In theory, this procedure is no different than any other simulation that one conducts. Check point file has velocity of the last co-ordinates and we are using middle configuration.. Thank you for explaination ... I have another query.. In npt equilibration can I use define = -DPOSRES (Position restrain all the protein along the chain B) and in production md define = -DPOSRES_B ( Position restrain for chain B only..) ??? If not What is appropriate reason??? You can use either. I have never tried it, but there is no reason to believe there will be any substantive reason during data collection. The production MD period is significantly longer than the equilibration, and the results will likely turn out the same, when considering error estimates. Sufficient sampling of any series of simulations should converge. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
Thank you Justin for giving your valuable time to solve my stupid problems. You can use either. I have never tried it, but there is no reason to believe there will be any substantive reason during data collection. The production MD period is significantly longer than the equilibration, and the results will likely turn out the same, when considering error estimates. Sufficient sampling of any series of simulations should converge. -Justin With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] REMD question
Dear Gromacs Users, We are implementing REMD method in Gromacs in protein folding, in your web page you give some steps that don´t mention any step about NPT stabilization. This step is necessary to run REMD simulations? Thank you in advance, Nathalia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] REMD question
Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibration at constant pressure. On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces natsgar...@gmail.com wrote: Dear Gromacs Users, We are implementing REMD method in Gromacs in protein folding, in your web page you give some steps that don´t mention any step about NPT stabilization. This step is necessary to run REMD simulations? Thank you in advance, Nathalia -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] GROMACS Installation problem: libfftw3f.so.3: cannot open shared object file
Dear Sir/Madam, Follow the steps below, I have installed fftw library and gromacs as a root. (1) tar -xzvf fftw-3.0.1.tar.gz(2) cd fftw-3.0.1(3) ./configure --enable-float --enable-threads --enable-shared(4) make(5) make install(6) tar -xzvf gromacs-4.5.5.tar.gz(7) cd gromacs-4.5.5(8) ./configure(9) make(10) make install(11) I have also add PATH=/usr/local/gromacs:$PATH; export PATH to my .bashrc file in my directory. However, I have problem to do the following comments: /usr/local/gromacs/bin/g_covar -s test.pdb -f test.netcdf -o -v The follow error message appears: /usr/local/gromacs/bin/g_covar: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such file or directory I found the following libraries in my /usr/local/lib directory: libfftw3f.a libfftw3f.so.3.0.1libfftw3f_threads.so.3 libfftw3f.lalibfftw3f_threads.a libfftw3f_threads.so.3.0.1libfftw3f.so libfftw3f_threads.la pkgconfiglibfftw3f.so.3 libfftw3f_threads.so Thus, it seems to me that libfftw3f.so.3 is already installed, whats' wrong with this? Could you mind to help. Best regards, Catherine -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS Installation problem: libfftw3f.so.3: cannot open shared object file
On 29/05/2012 3:09 PM, a a wrote: Dear Sir/Madam, Follow the steps below, I have installed fftw library and gromacs as a root. (1) tar -xzvf fftw-3.0.1.tar.gz (2) cd fftw-3.0.1 (3) ./configure --enable-float --enable-threads --enable-shared Here you enabled threads for fftw, which is not recommended here http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite. I don't know whether that's a problem, but certainly it will not help. (4) make (5) make install (6) tar -xzvf gromacs-4.5.5.tar.gz (7) cd gromacs-4.5.5 (8) ./configure (9) make (10) make install (11) I have also add PATH=/usr/local/gromacs:$PATH; export PATH to my .bashrc file in my directory. See http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation for the recommended procedure. However, I have problem to do the following comments: /usr/local/gromacs/bin/g_covar -s test.pdb -f test.netcdf -o -v /div The follow error message appears: /usr/local/gromacs/bin/g_covar: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such file or directory I found the following libraries in my /usr/local/lib directory: libfftw3f.a libfftw3f.so.3.0.1libfftw3f_threads.so.3 libfftw3f.lalibfftw3f_threads.a libfftw3f_threads.so.3.0.1 libfftw3f.solibfftw3f_threads.la pkgconfig libfftw3f.so.3 libfftw3f_threads.so Thus, it seems to me that libfftw3f.so.3 is already installed, whats' wrong with this? Could you mind to help. Your system apparently doesn't have this location in the search path for shared libraries. Maybe following http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation will fix that. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Measure of density in homo- and heterogeneous systems
Justin, the main problem is the my simulation in nvt ensemble :) I understand that density is constant in that conditions but I'd like to find way to check this values for different components of my system. James 2012/5/28 Justin A. Lemkul jalem...@vt.edu On 5/28/12 3:09 PM, James Starlight wrote: Dear Gromacs users! In this task I have two systems: First system consist of single layer of Ccl4 molecules. Second system consist of membrane-mimicking layer of Ccl4 surrounded by water and the protein embedded in that biphastic layer. I'd like to measure density in both of my systems to check of its packing degree. How could I do it in the case of homo system- (where I'd like to check density in the Ccl4 layer only) as well as in more complex hetero system ( where I'd like to check density in each layer separately as well as compute averaged density among all layers) ? The density of the homogeneous system can easily be obtained from the .edr file, as long as the ensemble was NPT. With NVT, the density term is not written, IIRC. In the case of the heterogeneous system, use g_density to obtain partial densities as a function of box dimension. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Measure of density in homo- and heterogeneous systems
On 29/05/2012 3:21 PM, James Starlight wrote: Justin, the main problem is the my simulation in nvt ensemble :) I understand that density is constant in that conditions but I'd like to find way to check this values for different components of my system. AFAIK, there's no easy way to do that with GROMACS tools. The problem lies in defining the shape over which you want to compute such a partial density, since you need to compute its volume. Any solution is likely to be at least a bit crude, even for a trivial case of a membrane-mimic in water whose interfaces are roughly orthogonal to a box vector. g_select may be useful in forming a suitable subset, and g_sas may be suitable for computing density and/or volume. Mark James 2012/5/28 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 5/28/12 3:09 PM, James Starlight wrote: Dear Gromacs users! In this task I have two systems: First system consist of single layer of Ccl4 molecules. Second system consist of membrane-mimicking layer of Ccl4 surrounded by water and the protein embedded in that biphastic layer. I'd like to measure density in both of my systems to check of its packing degree. How could I do it in the case of homo system- (where I'd like to check density in the Ccl4 layer only) as well as in more complex hetero system ( where I'd like to check density in each layer separately as well as compute averaged density among all layers) ? The density of the homogeneous system can easily be obtained from the .edr file, as long as the ensemble was NPT. With NVT, the density term is not written, IIRC. In the case of the heterogeneous system, use g_density to obtain partial densities as a function of box dimension. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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-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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Calculating number density using g_density
On 27/05/2012 2:00 AM, Andrew DeYoung wrote: Hi, It is possible to compute the number density using g_density, with the switch -dens number. Do you know if this is the number density of molecules? Or is it the number density of atoms? I'd expect atoms, but you should be able to test for this easily. Ideally, I would like to compute the number density of _molecules_. Specifically, I would like to use the center of mass of each molecule to represent that molecule's position. Then the center of mass of each molecule should be used to calculate the number density of molecules. Do you know if this is possible using any of the Gromacs utilities? Not natively. g_traj -com can compute centers of mass of groups, which you could assemble into a pseudo-trajectory using a script you wrote yourself. g_density -dens number should then work on molecules as you intend. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] charm in gromacs
On 18/05/2012 8:02 PM, francesco oteri wrote: Hi, at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can find the files I am using Files ffcharmmnb.itp ffcharmmbon.itp have been generated through: convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl/ par_all36_carb.prm while carbohydrates.rtp and carbohydrates.rtp through a script of mine. Now, if you look at [ dihedraltypes ] section in file ffcharmmbon.itp, there are strange things: 1) dihedrals defined once, are converted Ryckaert-Bellemans form, while the armonic form should be more clear. Anyway, it just a matter of style so I dont complan about. 2) dihedrals with multiple definitions ( OC30P CC3162 CC3161 OC311 at line 598 in file ffcharmmbon.itp, for example) are defined as: OC30P CC3162 CC3161 OC311 3 20.92 41.84 16.74 -41.84 0 0 ; 30P CC3162 CC3161 OC311 1 180 10.46 1 ; 30P CC3162 CC3161 OC311 1 0 8.368 2 ; 30P CC3162 CC3161 OC311 1 0 10.46 3 The commented lines clearly display the multiple definition, that can be described using function 9 ... which didn't exist at the time of my writing of that script, as the comments in the script discuss. Hence solution 1), which was adequate for the subset of CHARMM27 that was of interest to me. 3) An other problem rise with impropers dihedrals. Any of them are defined as Ryckaert-Bellemans, ex. HCA1 CC3161 CC3162 OC311 3 0.5858 1.757 0 -2.343 0 0 at line 926 of ffcharmmbon.itp while points 1 and 2 don't impact on the correctness of the simulation and can be bypassed defining [ bondedtypes ] section as following 1 5 321 3 1 0 Problem 3 cannot be solved without manipulating the ffcharmmbon.itp. In fact, since some impropers are defined as functiontype 2 other as functiontype 3, so there is not an unique bondedtypes definition covering both the definition. Did I any mistake or actually there is a problem in the script? IIRC CHARMM36 is more recent than that script, so the assumptions made by the script for CHARMM27 may not be applicable. If CHARMM36 uses more than one kind of improper dihedral, then I would not expect the script to function correctly in this regard. You would need to modify the script or its output. Mark Francesco 2012/5/18 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had no reason to upgrade these conversion scripts to support function type 9. Mark -- gmx-users mailing list 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] electrostatic component of the forces
Thank you very much for your clear reply. Best regards, Julian Garrec Le 25/05/12 17:17, Mark Abraham a écrit : On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote: Hi all, I am trying to get the electrostatic forces acting on each atom as a function of time. I have checked the list and all the suggestions are based on rerunning the simulation. Is there not an easy way to print these forces on the fly ? You can print the whole force on the fly with nstfout, but you cannot decompose it. If not, what is the cleanest way to remove bonded and vdw components from the forces ? One option could be to set all the unwanted interaction to zero in the topology file but I am wondering if there is a safer alternative. The code permits such a safe alternative, by not setting GMX_FORCE_BONDED, but there is no way to access that setting from the command line. The best you can easily do is mdrun -rerun with parameters zeroed. Mark -- Julian Garrec, post-doc Tel: ++41 (0)21 69 303 27 Web: https://sites.google.com/site/juliangarrec/ Laboratory of Computational Chemistry and Biochemistry BCH 4201 Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
