Re: [gmx-users] how to run charmm2gromacs-pvm.py correctly?
On 11/27/2012 07:43 PM, David van der Spoel wrote: On 2012-11-27 17:58, Albert wrote: Hello: I am trying to convert the output from CGenFF website into Gromacs .itp format by command: python charmm2gromacs-pvm.py charmm.rst you need an extra file. IIRC the cgenff method gives you two files. Hello: thanks for kind reply. In fact we get only one .str file from CGENFF server, and we have to split them into two files manually: In top_ligand.rtf (topology file): copy the lines between read rtf card append and the next END (both excluded). Manually modify the line starting with RESI in order to set your chosen residue name. This will be the name of the residue in the PDB file. In par_ligand.inp (parameter file): copy the lines between read param card flex append and the next END (both excluded). Now I generate the above two files and put them into the folder cgenff.ff, and run command: ./charmm2gromacs-pvm.py cgenff.ff but it still claimed: Traceback (most recent call last): File ./charmm2gromacs-pvm.py, line 33, in module parFile = open(sys.argv[2], 'r') IndexError: list index out of range -- 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] convergence problem
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Output of energy minimization step is like this. Reached the maximum number of steps before reaching Fmax 100 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 100 in 20001 steps. Potential Energy = -2.3055431e+05 Maximum force = 4.9160068e+02 on atom 3105 Norm of force = 8.8015385e+00 Is it wrong to do equilibration step further? and how to converge energy here? -- 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] About Diffusion of water Towards Tail part of Lipids
Dear Justin, Than you for your Previous reply Regarding Diffusion Of Water From Head of Lipids to Tail Part During NVT Equilibration, You Suggested My one question as follows May I freeze these molecules During NVT Equilibration) ? The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration in the absence of any restraints on water. My Question is If Need to use Restraint on Water . Should I Generate Separate water_posre.itp using genrestr tool ? Otherwise May I Edit ( it means Applying restraint only in fcz column and Making Zero for fcx and fcy columns ) and use Default setting of restraint of water in .top files as follows #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif Also How to include this Restraint in .mdp just Like using -D Flag ? Thanks In Advance -- 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] AU-S bonded parameter
hello I want add Au-S parameter for E(bond)=K*(r-r0)^2 to bonded parameters of OPLSAA forcefield. according to the paper, r0=2.4 A , k(au-s)=4180 [kJ/(mol/Å2)]. But in Gromacs manual K unit is KJ/mol. I dont understand it. for use of k(au-s), should I unitless it or not? meaning, I should multiple this K to sigma(au-s) and then put in bonded file? thank you Fatemeh Ramezani -- 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] Question about conserved energy in MTTK
Hi, I was also facing the same problem. If you check your pressure during this NPT run, u can see that it got increased to a higher value. I had posted the same problem few days back, u can follow the thread. It seems MTTK is not stable enough and is not performing well in this context. So I have moved to Leap-frog, Nose-Hoover, Parinello-Rahman combination for the NPT simulation. There is one paper as well by Prof. Shirts in JCTC. Cheers, Tarak On Thu, Nov 22, 2012 at 2:08 PM, Shun Sakuraba sakuraba.s...@jaea.go.jp wrote: Dear list, I am trying to use MTTK barostat in GROMACS 4.5.5. After analyzing the result for a while, I found that the conserved energy (not total energy) of MTTK is drifting during the simulation. The .xvg, .edr files are uploaded at [1] and [2]. It is drifting with a constant ratio of ca. -185 kJ/mol/ps. I cannot believe this is an expected behavior, so could anyone point out where I am wrong in my simulation setup? I found similar report at [3] but seems it was when 4.5 was in pre-release stage. Thanks in advance for your help! * Simulation detail The system consists of 1000 SPC-E water molecules, and the time step is set to 0.5 fs, just in case the long timestep harms the conserevation (c.f. [3]). The interaction energy is set to switching version, just in case, too. Changing these parameter does not seem to improve the conservation. The double precision version of GROMACS is used (single precision version also has the same problem). The system has been pre-equilibrated with Berendsen pressure coupling simulation with the same pressure and temperature. [1] https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg [2] https://www.dropbox.com/s/tg8butw39rmz8qk/mttk05.edr [3] http://lists.gromacs.org/pipermail/gmx-developers/2010-January/003979.html == .mdp file contents follow integrator = md-vv define = dt = 0.0005 nsteps = 100 ; 500 ps coulombtype = PME-Switch vdwtype = Switch pbc = xyz rlist = 1.2 rcoulomb = 1.0 rcoulomb_switch = 0.9 rvdw = 1.0 rvdw_switch = 0.9 nstlist = 1 tinit = 0 tcoupl = nose-hoover tc_grps = System tau_t = 0.5 ref_t = 300.0 nsttcouple = 1 pcoupl = MTTK pcoupltype = isotropic compressibility = 4.5e-5 ref_p = 1.01325 tau_p = 0.5 refcoord_scaling = no nstpcouple = 1 constraints = hbonds constraint_algorithm = LINCS nstxtcout = 100 nstlog = 100 nstenergy = 100 nstvout = 0 nstxout = 1000 -- Shun SAKURABA, Ph.D. Postdoc @ Molecular Modeling Simulation Group, Japan Atomic Energy Agency -- 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] Vizualization with VMD: no image appears
vmd protein.trr protein.gro then go to the representation and then write 'all not water' with cartoon representation, u will get the protein only. Cheers, Tarak On Thu, Nov 22, 2012 at 12:58 PM, rama david ramadavidgr...@gmail.com wrote: Dear, -o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file. And then load it in vmd or pymol u can see it On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix frau...@ipb-halle.dewrote: Hi. Try to load in a .gro file of your system first. After that, use the load data into molecule option to load in the .xtc. -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von shch406 Gesendet: Mittwoch, 21. November 2012 17:47 An: gmx-users@gromacs.org Betreff: [gmx-users] Vizualization with VMD: no image appears Dear Gromacs users To visualize my trajectory with VMD I applied trjconv to .xtc trajectory file to eliminate water molecules and velocities remaining protein coordinates only. However, when I load this reduced file to VMD no image on screen appears, nevertheless VMD have identified the file as a Gromacs compress trajectory file. What may be the cause of this? The corresponding command is as follows: trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel where MT.xtc contains ~10 frames, defau.ndx is default groups index file. Group 2 (Protein-H) was chosen handling dialog. Merci pour votre collaboration, Igor Shchechkin -- View this message in context: http://gromacs.5086.n6.nabble.com/Vizualization-with-VMD-no-image-appears-tp5003167.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 -- 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] Re: About Temperature coupling and Energy Transfer....
On 11/28/12 12:11 AM, cyberjhon wrote: Dear Justin Thanks for your answer. I know what you mean, but the problem is that this is not a possible physical (real) behaviour. If the temperature is not controlled as you said, the energy should continue growing not stop, but in these case after 50ps it reaches some kind of equilibrium and stabilize. So why this is happening? Can you give me with a Physical or and Algorithmic answer? I'm guessing a bit here, because what you're doing is something that these algorithms were not intended to do. You have a warm solvent and a protein whose temperature is unregulated, so the protein acts as a heat sink and has energy transferred into it in an uncontrolled way. Maybe the algorithm finds a happy place at the temperature where it stabilizes, or maybe it's a failure of the thermostat that doesn't lead to a fatal error. -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] About the biotin parameter.....
On 11/28/12 12:20 AM, rama david wrote: Hi justin, Thank you for your suggestion. I read the ATB paper but the paper does not mention any thing related to the biotin. Probably not, it's too complex to be considered a model compound. When I mail them, they replied .. To clarify the validation: There are different levels of validation criteria used in the ATB. The one which is available on the ATB web-site for a given molecule is the validation of the topology against the compatibility with the GROMOS force field. The output contains energies for bonded parameters. The validation described in the paper is the validation against the experimental hydration free energy of small organic molecules. Biotin was not a part of the validation dataset. What should I have to do..??? Validation of a method (i.e., the ATB algorithm) and validation of the resulting parameters are different concepts. It is still incumbent upon you to demonstrate that the parameters you got from somewhere else (i.e., ATB) are suitable for what you intend. If you were to manually derive the parameters, you'd have to do the same thing. There is no guarantee that any service (PRODRG, ATB, etc) are inherently correct. ATB is generally quite good, but any reviewer worth his salt is going to ask whether or not you have evidence that the biotin parameters you chose are actually going to represent reality before you go spending a lot of time running simulations, collecting data, and making conclusions. The underlying validation of Gromos96 parameters involves calculating free energies of solvation for model compounds, which are then mapped back to the desired molecule (usually some biomolecule like an amino acid). So, in theory, you could: 1. Calculate the free energy of solvation of biotin, if it is known 2. Run test simulations of biotin in your protein and verify that it engages in known interactions Those are just what come to mind immediately, but you should consult the literature for other cofactors and see how they were parameterized. Gromos96 includes parameters for ATP, FAD, FMN, and others, so clearly there is methodology somewhere to which you can refer. -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] convergence problem
On 11/28/12 4:20 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Output of energy minimization step is like this. Reached the maximum number of steps before reaching Fmax 100 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 100 in 20001 steps. Potential Energy = -2.3055431e+05 Maximum force = 4.9160068e+02 on atom 3105 Norm of force = 8.8015385e+00 Is it wrong to do equilibration step further? and how to converge energy here? I've never reached an Fmax 100 for a membrane protein system. Likely your result is stable enough to proceed. -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] About Diffusion of water Towards Tail part of Lipids
On 11/28/12 4:24 AM, vidhya sankar wrote: Dear Justin, Than you for your Previous reply Regarding Diffusion Of Water From Head of Lipids to Tail Part During NVT Equilibration, You Suggested My one question as follows May I freeze these molecules During NVT Equilibration) ? The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration in the absence of any restraints on water. My Question is If Need to use Restraint on Water . Should I Generate Separate water_posre.itp using genrestr tool ? Otherwise May I Edit ( it means Applying restraint only in fcz column and Making Zero for fcx and fcy columns ) and use Default setting of restraint of water in .top files as follows #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif Modifying this section of the topology is the easiest thing to do. I see no reason to run genrestr. Also How to include this Restraint in .mdp just Like using -D Flag ? All #includes and defines work the same way. -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] AU-S bonded parameter
On 11/28/12 4:38 AM, fatemeh ramezani wrote: hello I want add Au-S parameter for E(bond)=K*(r-r0)^2 to bonded parameters of OPLSAA forcefield. according to the paper, r0=2.4 A , k(au-s)=4180 [kJ/(mol/Å2)]. But in Gromacs manual K unit is KJ/mol. I dont understand it. Energies are kJ/mol. Force constants are kJ/(mol-nm^2). Refer to the form of potential energy for a harmonic bond and the units become clear. for use of k(au-s), should I unitless it or not? meaning, I should multiple this K to sigma(au-s) and then put in bonded file? thank you All you need here is proper unit conversion (A - nm). Mind the square term (A^2 - nm ^2), which people often forget. -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] About the biotin parameter.....
Hi justin thank you for suggestion. I think to Calculate the free energy of solvation of biotin, I hve to use the method as per your tuotorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Is these right or I have to do anything else??? With Best Wishes and regards, Rama david On Wed, Nov 28, 2012 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/12 12:20 AM, rama david wrote: Hi justin, Thank you for your suggestion. I read the ATB paper but the paper does not mention any thing related to the biotin. Probably not, it's too complex to be considered a model compound. When I mail them, they replied .. To clarify the validation: There are different levels of validation criteria used in the ATB. The one which is available on the ATB web-site for a given molecule is the validation of the topology against the compatibility with the GROMOS force field. The output contains energies for bonded parameters. The validation described in the paper is the validation against the experimental hydration free energy of small organic molecules. Biotin was not a part of the validation dataset. What should I have to do..??? Validation of a method (i.e., the ATB algorithm) and validation of the resulting parameters are different concepts. It is still incumbent upon you to demonstrate that the parameters you got from somewhere else (i.e., ATB) are suitable for what you intend. If you were to manually derive the parameters, you'd have to do the same thing. There is no guarantee that any service (PRODRG, ATB, etc) are inherently correct. ATB is generally quite good, but any reviewer worth his salt is going to ask whether or not you have evidence that the biotin parameters you chose are actually going to represent reality before you go spending a lot of time running simulations, collecting data, and making conclusions. The underlying validation of Gromos96 parameters involves calculating free energies of solvation for model compounds, which are then mapped back to the desired molecule (usually some biomolecule like an amino acid). So, in theory, you could: 1. Calculate the free energy of solvation of biotin, if it is known 2. Run test simulations of biotin in your protein and verify that it engages in known interactions Those are just what come to mind immediately, but you should consult the literature for other cofactors and see how they were parameterized. Gromos96 includes parameters for ATP, FAD, FMN, and others, so clearly there is methodology somewhere to which you can refer. -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] About the biotin parameter.....
On 11/28/12 8:08 AM, rama david wrote: Hi justin thank you for suggestion. I think to Calculate the free energy of solvation of biotin, I hve to use the method as per your tuotorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Is these right or I have to do anything else??? That is the general workflow, though the .mdp settings will need to be modified and you will need to do both van der Waals and Coulombic transformations. I would also assume that you will need longer simulations and more lambda points to define the transformation, since biotin is considerably more complex than methane. -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] About the biotin parameter.....
Hi justin, Thank you for help With Best wishes and Regards, Rama david On Wed, Nov 28, 2012 at 7:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/12 8:08 AM, rama david wrote: Hi justin thank you for suggestion. I think to Calculate the free energy of solvation of biotin, I hve to use the method as per your tuotorial http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/free_energy/**index.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Is these right or I have to do anything else??? That is the general workflow, though the .mdp settings will need to be modified and you will need to do both van der Waals and Coulombic transformations. I would also assume that you will need longer simulations and more lambda points to define the transformation, since biotin is considerably more complex than methane. -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
[gmx-users] On the usage of SD integrator as the thermostat
By 'proper dynamics' I mean the correct dynamics. For example, if a simulation with the SD integrator indicates that loop1 folds before loop2 folds, then this might be incorrect. The state information will be correct in velocity Langevin dynamics but the dynamic information might be incorrect. The advantage of the SD integrator over the Berendsen thermostat is that you get the correct ensemble. Check out papers by Garcia in relation to the flying ice cube problem and lipid bilayers. Is the same thing true for Nose-Hoover? I am not sure, but I am sure that you can find out. I recall hearing that the Nose-Hoover thermostat is very sensitive to propagating and magnifying temperature fluctuations. Chris. -- original message -- I am wondering what you mean by 'proper dynamics', Chris? And in general, what's the advantage of using sd integrator over md integrator together with Nose-Hoover thermostat. Thanks, km. On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale chris.neale at mail.utoronto.ca wrote: I use the SD integrator with tau_t = 1.0 ps for all of my work, including proteins in aqueous solution or embedded in a lipid membrane. Any value of tau-t is correct, and none will give you the proper dynamics, but I find that the diffusion of both water and lipids is quite reasonable when using tau_t=1.0 ps. I arrived at 1.0 ps after some help from Berk Hess on this list. I suggest that you search out those old posts. Chris. -- original message -- In manual I've found possibility of the usage of the sd (langeven's dynamics) integrator as the thermostat. It's known that friction coefficient in the Langeven's equations is defined as m/Tau_t. So the high values of tau t can be appropriate for the modeling of the thermostat without t_coupl. Also I know that friction coefficient for such simulation must corresponds to the viscosity of the system. In Gromacs manual I've found that Tau-t= 2.0 ps can be appropriate value for such simulations. Does this value suitable for water-soluble system only ? What Tau_t should I use for modeling of the membrane proteins in the lipid-water environment which has higher viscosity ? Thanks for help, 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
Re: [gmx-users] Question about conserved energy in MTTK
Hi, all- I would recommend using Parrinellio-Rahman + Nose-Hoover md + at least until 4.6. A random-walk drift in the conserved energy is actually what MTTK gives -- it's not as conserved as, say, energy conservation, it just has an expectation value of zero drift over time, which means that the RMSD will increase with time according to sqrt(dt). But if you are seeing constant drift, something is wrong. On Wed, Nov 28, 2012 at 7:20 AM, tarak karmakar tarak20...@gmail.com wrote: Hi, I was also facing the same problem. If you check your pressure during this NPT run, u can see that it got increased to a higher value. I had posted the same problem few days back, u can follow the thread. It seems MTTK is not stable enough and is not performing well in this context. So I have moved to Leap-frog, Nose-Hoover, Parinello-Rahman combination for the NPT simulation. There is one paper as well by Prof. Shirts in JCTC. Cheers, Tarak On Thu, Nov 22, 2012 at 2:08 PM, Shun Sakuraba sakuraba.s...@jaea.go.jp wrote: Dear list, I am trying to use MTTK barostat in GROMACS 4.5.5. After analyzing the result for a while, I found that the conserved energy (not total energy) of MTTK is drifting during the simulation. The .xvg, .edr files are uploaded at [1] and [2]. It is drifting with a constant ratio of ca. -185 kJ/mol/ps. I cannot believe this is an expected behavior, so could anyone point out where I am wrong in my simulation setup? I found similar report at [3] but seems it was when 4.5 was in pre-release stage. Thanks in advance for your help! * Simulation detail The system consists of 1000 SPC-E water molecules, and the time step is set to 0.5 fs, just in case the long timestep harms the conserevation (c.f. [3]). The interaction energy is set to switching version, just in case, too. Changing these parameter does not seem to improve the conservation. The double precision version of GROMACS is used (single precision version also has the same problem). The system has been pre-equilibrated with Berendsen pressure coupling simulation with the same pressure and temperature. [1] https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg [2] https://www.dropbox.com/s/tg8butw39rmz8qk/mttk05.edr [3] http://lists.gromacs.org/pipermail/gmx-developers/2010-January/003979.html == .mdp file contents follow integrator = md-vv define = dt = 0.0005 nsteps = 100 ; 500 ps coulombtype = PME-Switch vdwtype = Switch pbc = xyz rlist = 1.2 rcoulomb = 1.0 rcoulomb_switch = 0.9 rvdw = 1.0 rvdw_switch = 0.9 nstlist = 1 tinit = 0 tcoupl = nose-hoover tc_grps = System tau_t = 0.5 ref_t = 300.0 nsttcouple = 1 pcoupl = MTTK pcoupltype = isotropic compressibility = 4.5e-5 ref_p = 1.01325 tau_p = 0.5 refcoord_scaling = no nstpcouple = 1 constraints = hbonds constraint_algorithm = LINCS nstxtcout = 100 nstlog = 100 nstenergy = 100 nstvout = 0 nstxout = 1000 -- Shun SAKURABA, Ph.D. Postdoc @ Molecular Modeling Simulation Group, Japan Atomic Energy Agency -- 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 -- 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] Hbonds between Adenine and Thymine
Dear Gromacs users, I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 ns. After a while Thymine rotated for about 70 degrees and then returned to its initial position. I wanted to find out hbonds between Adenine and Thymine but with make_ndx things don't work so well. How can I select Adenine from one strand and Thymine from the other strand and then run g_hbond ? Thanks in Advance Best regards, Hovakim Grabski -- 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] Bonded parametrs for CG
On Thu, Nov 22, 2012 at 12:27 PM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, What is the best way to extract bonded parameters from all atom simulation for the coarse grained model in gmx? One posibility is starting with ad-hoc parameters, e.g. equilibrium distances from the optmized AA structure converted to CG and ad-hoc force constants, and tune them iteratively by comparing the bond length, angle bend and dihedral distributions from the CG simulation with an atomistic trajectory converted to CG. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- 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] Hbonds between Adenine and Thymine
On 11/28/12 3:43 PM, Hovakim Grabski wrote: Dear Gromacs users, I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 ns. After a while Thymine rotated for about 70 degrees and then returned to its initial position. I wanted to find out hbonds between Adenine and Thymine but with make_ndx things don't work so well. How can I select Adenine from one strand and Thymine from the other strand and then run g_hbond ? You can use make_ndx to select any residues you want. You'll have to describe exactly what you did that produced insufficient results. Saying it didn't work well doesn't tell us anything, because it is in fact quite easy to produce usable index groups. -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] mixed single-precision GPU and double-precision CPU calculation
Dear GROMACS peoples: I know the current gromacs-4.6 can't build with both GPU and double precision being enable. I'm wondering is it possible to modify mixed single-precision (non-bonded) GPU calculation and double-precision CPU calculation? I suppose this combination would be practically useful when we needs high precision constraint calculation (with SHAKE or LINCS etc.). If it is possible by modifying some routine, please teach me the routine to modify. I would like to try it. Thank you for advance. Makoto Yoneya, Dr. AIST, Japan Makoto Yoneya, Dr. http://staff.aist.go.jp/makoto-yoneya/ -- 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 4.6 segmentation fault with mdrun
Dear Makoto Yoneya, Thank you for the feedback, it is of great help! I will try to reproduce the issue because mdrun should not segfault with any gcc version 4.3 and above. Could you please provide two more things: - a log file of the failed run using the latest code from git; - run mdrun with the -debug 1 option, 0 steps is enough and provide the mdrun.debug output? These would be very useful to know the exact software setup you are using (detailed information in the new header of the mdrun's log files) and the location of the crash (based on the debug output). (Large?) Attachments might still be turned off for the list so please upload the files somewhere and send us a link (pastebin or a similar service is fine). Thank you in advance, -- Szilárd On Tue, Nov 27, 2012 at 11:43 PM, Makoto Yoneya makoto-yon...@aist.go.jpwrote: Dear GROMACS users: On Gromacs 4.6 segmentation fault with mdrun, I'd also met the same segmentation fault problem with gromacs-4.6. on my linux box with GTX-580. For my case, change the compilor solved this problem. Raf Ponsaerts wrote he used gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1 CMake 2.8.7 . These were same in the version when I first met the problem. After that, I'd tried Intel compilor instead of gcc-4.4.x, then the GPU jobs runs without the segmentation fault. I also tried gcc-4.6.x and it also runs without any faults (I'm using CentOS and its gcc version is currentry gcc-4.4.x. Then, I had to compile gcc-4.6.x from the source. gcc-4.7.x can't use with CUDA-4.2 since it only suppoorts up to gcc-4.6.x.). I suggest to try either intel compilor or gcc-4.6.x instead of gcc-4.4.x. Makoto Yoneya, Dr. AIST, Japan -- 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
[gmx-users] gromacs 4.5.5 Do_dssp segment fault
When I use the Do_dssp module to collect the data from --.trr ,It report segment fault. The other common module is normol.WHY?? Thanks! -- xiaohong-- 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 4.5.5 Do_dssp segment fault
On 11/28/12 9:21 PM, Kdead wrote: When I use the Do_dssp module to collect the data from --.trr ,It report segment fault. The other common module is normol.WHY?? Thanks! The input options in the DSSP executable changed. This is a known problem and has been around for a long time. Your options are: 1. Obtain an old version of DSSP 2. Apply the patch described in the mailing list archive or otherwise install the development version via git 3. Wait for the first beta release of version 4.6, where this problem is fixed (should be released very soon) -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] what does it mean by 'started run on node 0'
Dear Sir/Madam I am very sorry to interrupt you again, but now I came across some problem haven't checked out what was going wrong. I used Matlab to established the DNA and graphene nanosheet model including all the .gro files, .itp files and .top files. When I ran it, the computer didn't send out error information, but it just has no calculations, I attached my md.log file so could you please take a look for me? (there is one sentence in the end of the log file, saying that started mdrun on node 0 , I don't know why) I would really appreciate your kindly help, looking forward to your reply. Best regards -- 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] error during nvt equilibration
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration and created index.ndx by using make_ndx. During this step I selected 16/14 and 1/13.The next step (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr) getting error like this Fatal error: Group SOL_CL 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. why this error? Can you give a solution to overcome it? -- 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] Question about conserved energy in MTTK
Hi, Thank you for replies. I was also facing the same problem. If you check your pressure during this NPT run, u can see that it got increased to a higher value. In my case, the situation looks slightly different. The pressure is not increasing at all (see xvg file in [1]), though it is only 500-ps simulation. It is also averaged to the target pressure of 1.0. For my case, the only problem is the constant drift of the conserved energy, and everything others look at least reasonable to me. But if you are seeing constant drift, something is wrong. Yes, it is constantly drifting. Is it better to file a report to redmine? [1] https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg On 2012年11月29日 02:07, Michael Shirts wrote: Hi, all- I would recommend using Parrinellio-Rahman + Nose-Hoover md + at least until 4.6. A random-walk drift in the conserved energy is actually what MTTK gives -- it's not as conserved as, say, energy conservation, it just has an expectation value of zero drift over time, which means that the RMSD will increase with time according to sqrt(dt). But if you are seeing constant drift, something is wrong. On Wed, Nov 28, 2012 at 7:20 AM, tarak karmakar tarak20...@gmail.com wrote: Hi, I was also facing the same problem. If you check your pressure during this NPT run, u can see that it got increased to a higher value. I had posted the same problem few days back, u can follow the thread. It seems MTTK is not stable enough and is not performing well in this context. So I have moved to Leap-frog, Nose-Hoover, Parinello-Rahman combination for the NPT simulation. There is one paper as well by Prof. Shirts in JCTC. Cheers, Tarak On Thu, Nov 22, 2012 at 2:08 PM, Shun Sakuraba sakuraba.s...@jaea.go.jp wrote: Dear list, I am trying to use MTTK barostat in GROMACS 4.5.5. After analyzing the result for a while, I found that the conserved energy (not total energy) of MTTK is drifting during the simulation. The .xvg, .edr files are uploaded at [1] and [2]. It is drifting with a constant ratio of ca. -185 kJ/mol/ps. I cannot believe this is an expected behavior, so could anyone point out where I am wrong in my simulation setup? I found similar report at [3] but seems it was when 4.5 was in pre-release stage. Thanks in advance for your help! * Simulation detail The system consists of 1000 SPC-E water molecules, and the time step is set to 0.5 fs, just in case the long timestep harms the conserevation (c.f. [3]). The interaction energy is set to switching version, just in case, too. Changing these parameter does not seem to improve the conservation. The double precision version of GROMACS is used (single precision version also has the same problem). The system has been pre-equilibrated with Berendsen pressure coupling simulation with the same pressure and temperature. [1] https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg [2] https://www.dropbox.com/s/tg8butw39rmz8qk/mttk05.edr [3] http://lists.gromacs.org/pipermail/gmx-developers/2010-January/003979.html == .mdp file contents follow integrator = md-vv define = dt = 0.0005 nsteps = 100 ; 500 ps coulombtype = PME-Switch vdwtype = Switch pbc = xyz rlist = 1.2 rcoulomb = 1.0 rcoulomb_switch = 0.9 rvdw = 1.0 rvdw_switch = 0.9 nstlist = 1 tinit = 0 tcoupl = nose-hoover tc_grps = System tau_t = 0.5 ref_t = 300.0 nsttcouple = 1 pcoupl = MTTK pcoupltype = isotropic compressibility = 4.5e-5 ref_p = 1.01325 tau_p = 0.5 refcoord_scaling = no nstpcouple = 1 constraints = hbonds constraint_algorithm = LINCS nstxtcout = 100 nstlog = 100 nstenergy = 100 nstvout = 0 nstxout = 1000 -- Shun SAKURABA, Ph.D. Postdoc @ Molecular Modeling Simulation Group, Japan Atomic Energy Agency -- 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 -- Shun SAKURABA, Ph.D. Postdoc @ Molecular Modeling Simulation Group, Japan Atomic Energy Agency -- 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
