[gmx-users] gromacs on GPU
Dear Gromacs Users! I want to install gromacs 4.55 on my Debian OS with the GPU support (I'd like to make some calculations on the GeForce 670 gpu). I have cuda-toolkit as well as openMM 4.01 installed from the binaries as well as gromac's sources. Could you provide me with some tutorial where I could found such step-by-step installation of the Gromacs with gpu. 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
[gmx-users] Re: gold-protein simulation
Dear Justin What you said is true for bonded parameters, but how about the parameters of the nonbonded file? Why Despite any non-bonded parameters (Sigma, Epsilon) are considered between the gold atom and the other atoms , protein is stretched to the gold cluster ? What is the reason for this closing?Is not it true that when there is no epsilon and Sygma between two atoms, should not be move toward one another? 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] Fatal error: Number of atoms in Topology is not the same as in Trajectory
On 1/6/13 1:00 AM, Shima Arasteh wrote: I ran NPT equilibration for 1ns. Would that be ok if I rerun it for 1 or more ns ? I have no idea what will be necessary for your system. That's up to you to analyze and determine. -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] gromacs on GPU
On 1/6/13 4:48 AM, James Starlight wrote: Dear Gromacs Users! I want to install gromacs 4.55 on my Debian OS with the GPU support (I'd like to make some calculations on the GeForce 670 gpu). I have cuda-toolkit as well as openMM 4.01 installed from the binaries as well as gromac's sources. Could you provide me with some tutorial where I could found such step-by-step installation of the Gromacs with gpu. http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs#Installing_and_running_GROMACS-GPU -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: gold-protein simulation
On 1/6/13 5:12 AM, fatemeh ramezani wrote: Dear Justin What you said is true for bonded parameters, but how about the parameters of the nonbonded file? Why Despite any non-bonded parameters (Sigma, Epsilon) are considered between the gold atom and the other atoms , protein is stretched to the gold cluster ? What is the reason for this closing?Is not it true that when there is no epsilon and Sygma between two atoms, should not be move toward one another? You should probably have sigma and epsilon values for all interactions. If you don't have any (are they set to zero?) then likely the motion you're seeing is just random because there's no other driving force unless charges are involved. In that case, you have basically unscreened Coulombic interactions, which likely aren't a very good model for anything, but I've never done any sort of gold simulations, so I don't know what people do in that case. -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] (no subject)
I didn't set epsilon and sigma between au and other atoms equal to zero, but I have not enteredanyEpsilon and Sigmafor them , and once again I set them zero and try it again. But if closing of gold to protein, is because of charge, how do I delete its effect ? How can I uncharged the system? (Of course, the whole system charge that is shown in the first grompp step is very low near -0.11). 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] gromacs on GPU
Have someone tried to use gromacs-4.5-gpu binaries ? Would that packages work on debian or its better to build from sources ? :) James 2013/1/6 Justin Lemkul jalem...@vt.edu: On 1/6/13 4:48 AM, James Starlight wrote: Dear Gromacs Users! I want to install gromacs 4.55 on my Debian OS with the GPU support (I'd like to make some calculations on the GeForce 670 gpu). I have cuda-toolkit as well as openMM 4.01 installed from the binaries as well as gromac's sources. Could you provide me with some tutorial where I could found such step-by-step installation of the Gromacs with gpu. http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs#Installing_and_running_GROMACS-GPU -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 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: Simulation of 2D lattice model
I mean absence of exponential factor in the C6 term :) So to change the vdw radius of the specified atom I should to varry both c6 and c12 shouldn't it ? James 2013/1/5 Justin Lemkul jalem...@vt.edu: so it may complicate such correction in that ff. What's wrong with it? -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 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 subject)
On 1/6/13 7:29 AM, fatemeh ramezani wrote: I didn't set epsilon and sigma between au and other atoms equal to zero, but I have not enteredanyEpsilon and Sigmafor them , and once again I set them zero and try it again. If you didn't set them at all, grompp should have given a fatal error. But if closing of gold to protein, is because of charge, how do I delete its effect ? How can I uncharged the system? (Of course, the whole system charge that is shown in the first grompp step is very low near -0.11). If your system has a net charge of -0.11, the topology is incorrect. Fractional charges on the system are nonphysical. -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] gromacs on GPU
On 1/6/13 7:41 AM, James Starlight wrote: Have someone tried to use gromacs-4.5-gpu binaries ? Would that packages work on debian or its better to build from sources ? :) The binaries online are very outdated. Compiling from source is rather easy, and the website below has all the steps listed. -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: Simulation of 2D lattice model
On 1/6/13 7:44 AM, James Starlight wrote: I mean absence of exponential factor in the C6 term :) Values can be represented as normal decimals or in scientific notation. So to change the vdw radius of the specified atom I should to varry both c6 and c12 shouldn't it ? If you want to derive a new atom type, sure. I still don't understand why this is necessary, though - people simulate graphene and similar structures routinely using existing force fields. If you feel the force field is inadequate, by all means go through the process to derive whatever you think is better. -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: Simulation of 2D lattice model
On Sun, Jan 6, 2013 at 1:44 PM, James Starlight jmsstarli...@gmail.com wrote: I mean absence of exponential factor in the C6 term :) So to change the vdw radius of the specified atom I should to varry both c6 and c12 shouldn't it ? Hmm, to me these look like very basic force field questions. Did you try to look the Lennard-Jones potential in a good MD book ? Or in the vast amount of resources available for free online ? Or, even better, in the GROMACS manual ? That would take surely less than an hour, while your questions on the subject have stretched over several days. The 6-12 LJ potential is composed of an attractive and repulsive term. The 6-12 combination is often used because of computational efficiency, as the 12-term can be obtained by multiplying the 6-term with itself. Each of these terms has a constant, typically called C6 and C12, which tells how much each term contributes to the total potential. For example, to have only the 6-term, C12 can be set to zero - this is useful when one knows how much attractive and how much repulsive the potential should be. Most often though, one thinks of the LJ potential in terms of equilibrium distance (obtained through a combination rule) and potential well, expressed through the sigma and epsilon constants. The two pairs (C6/C12 and sigma/epsilon) are interrelated. The relation is given in the GROMACS manual, on the Wikipedia page related to the LJ potential and in many other places. GROMACS also comes with a tool (g_sigeps) which allows an easy transformation between them. As you can see from the formulas, sigma depends on both C6 and C12 and epsilon depends on both C6 and C12. So, to partly answer your question, to change the equilibrium distance (sigma) you need to vary both C6 and C12. It's only partly answered because you need to read about combination rules in the GROMACS manual to see how to get from the atom radius to LJ potential sigma... Please note that a particular force field uses only one of the pairs (C6/C12 or sigma/epsilon) - you can't mix and match. If you want to use f.e. OPLS-AA, all LJ interactions are expressed using the sigma/epsilon pair. If you want to introduce in this force field a new type of interaction based on another force field which is defined using the C6/C12 pair, you have to perform the conversion to sigma/epsilon. If, on the other hand, you design your own force field, you are free to use either of the two pairs but, once chosen, you have to be consistent and use that pair for all LJ interactions. Cheers, Bogdan -- 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 on GPU
OK! I've compilated gromacs-gpu from the source using that tutorial for the Debian OS http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html The only thing that it lack is the installation mdrun_d-gpu but i'm not sure that double precission can be used with gpu. Could someone provide me with some tutorial which would show me basic mdrun options with the calculation on my gpu as well as some testing system? James 2013/1/6 Justin Lemkul jalem...@vt.edu: On 1/6/13 7:41 AM, James Starlight wrote: Have someone tried to use gromacs-4.5-gpu binaries ? Would that packages work on debian or its better to build from sources ? :) The binaries online are very outdated. Compiling from source is rather easy, and the website below has all the steps listed. -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 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 on GPU
On 1/6/13 1:53 PM, James Starlight wrote: OK! I've compilated gromacs-gpu from the source using that tutorial for the Debian OS http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html The only thing that it lack is the installation mdrun_d-gpu but i'm not sure that double precission can be used with gpu. Could someone provide me with some tutorial which would show me basic mdrun options with the calculation on my gpu as well as some testing system? Everything you need to know (including benchmark systems) is posted at http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs. The invocation of mdrun-gpu is like any other mdrun, with GPU-specific information available by reading mdrun-gpu -h. -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] simulating protein in gas-phase
Dear Gromacs users, I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and ligand in gas phase. I have previously run the simulation in water without any problem. Now, I want to compare the result to see the effect of solvent. But for running the same simulation after stripping the waters from the simulation box I am looking for some advise. I am having following issues: a) If I use 'md' i.e usual leap frog integrator with nstcomm=10 and comm-mode=Linear( this was the setup I had when I ran the simulation in water), I find after running the system of protein and ligand in gas phase for some time ( about 1 ns ), the protein starts rotating i.e it generates a very high angular momentum. b) So, I thought of using comm-mode=angular,,, But then grompp gives me a warning that removing rotation is not a problem only if I have only 1 molecule in the system ...which is not the case here as I have ligand and some ions . Any suggestion is highly appreciated. I can change nstcomm=1 using comm-mode=Linear but I am not sure it will stop the rotation of the protein about its own axis. I am running the system using periodic boundary condition and using PME for electrostatics. c) another option I thought of was using 'sd' integrator but considering my simulation in water having been performed using md integrator, I was looking to keep my .mdp file option as similar as possible in both cases. Any help on how to perform the simulations in gas-phase will be highly appreciated. Here is my current .mdp options: title = Umbrella pulling simulation ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 150 ; 800 ps nstcomm = 10 ; Output parameters nstxout = ; every 10 ps nstvout = nstfout = nstxtcout = 250 nstenergy = 250 ; Bond parameters constraint_algorithm = lincs constraints = hbonds continuation = yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = System tau_t = 0.5 ref_t = 300 ; Pressure coupling is on Pcoupl = no pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on gen_vel = yes ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres Thanks Sanku -- 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] Reducing trr storage volume
You can construct such a subset after the fact by using trjconv with (say) an index group created with g_select, but you will have to script that process frame by frame yourself. Mark On Fri, Jan 4, 2013 at 9:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/4/13 11:09 AM, Shima Arasteh wrote: Dear users, I'm simulating a system of protein/water/popc/ions. The peptide is inserted through the transmembrane, and the peptide acts as a channel. In order to reduce the trajectory storage volume, I need to use xtc-grps in .mdp file. In my system, I'd rather to store the positions of peptide,ions and waters near the peptide (I mean a specific region near the peptide: entrances of peptide + through the peptide).The large amount of water molecules positions exist up and down the bilayer, are not expected to be saved. I'm wondering if it is possible to chose a specific region in xtc-groups? Or any other solution to reduce the storage volume of trr file? I doubt you can achieve such a group consistently. Water molecules will diffuse over time. Index groups provided to grompp can only be specified to be a fixed size and cannot be dynamically created to satisfy any geometric criterion during mdrun. Thus, your initial group may indeed represent the desired molecules, but over time, the waters within the group will (likely) drift away and may not be anywhere near the original position. If your system contains a lot of water that you deem unnecessary, perhaps you should consider the manner in which the system was constructed... The only way to decrease the size of a .trr file is to decrease nstxout, nstvout, and/or nstfout. For various technical reasons, there is no way to save only a subset of atoms in .trr format. Refer to previous discussions on this topic. -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] selecting res CYS from G53a5 using pdb2gmx
Hi, I am using gromacs 4.5.4, and I am generating a topology file using G53a5 force field. My protein has a Cys residue which is supposed to be in thiolate state (negatively charged side chain). During issuing the pdb2gmx command I use the switch -inter to be prompted about the charge state of the ionisable side chains, but it asks nothing about Cys side chains except about they being involved in disulfide bonds. My questions are: 1. how can I get pdb2gmx ask me about the charge status of Cys residues? Or do I need to manually change their status in the topology file and output gro file (removing the HG)? 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, the total charge of the residue does not add to -1 but -0.5. Is anyone aware of any modifications to this force field parameters? Best, Payman -- 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] Calculating the helix moments
Dear users, I want to know how to calculate 1. The rotation angle of helix moments ? 2. number of water molecules interaction with ligand throughout the MD course ? 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
Re: [gmx-users] simulating protein in gas-phase
On 1/6/13 3:09 PM, Sanku M wrote: Dear Gromacs users, I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and ligand in gas phase. I have previously run the simulation in water without any problem. Now, I want to compare the result to see the effect of solvent. But for running the same simulation after stripping the waters from the simulation box I am looking for some advise. I am having following issues: a) If I use 'md' i.e usual leap frog integrator with nstcomm=10 and comm-mode=Linear( this was the setup I had when I ran the simulation in water), I find after running the system of protein and ligand in gas phase for some time ( about 1 ns ), the protein starts rotating i.e it generates a very high angular momentum. b) So, I thought of using comm-mode=angular,,, But then grompp gives me a warning that removing rotation is not a problem only if I have only 1 molecule in the system ...which is not the case here as I have ligand and some ions . Any suggestion is highly appreciated. I can change nstcomm=1 using comm-mode=Linear but I am not sure it will stop the rotation of the protein about its own axis. Use comm-mode = angular. I am running the system using periodic boundary condition and using PME for electrostatics. You're certain to get periodicity artifacts. You should run without PBC and with infinite cutoffs for nonbonded interactions to simulate the molecules in vacuo. -Justin c) another option I thought of was using 'sd' integrator but considering my simulation in water having been performed using md integrator, I was looking to keep my .mdp file option as similar as possible in both cases. Any help on how to perform the simulations in gas-phase will be highly appreciated. Here is my current .mdp options: title = Umbrella pulling simulation ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 150 ; 800 ps nstcomm = 10 ; Output parameters nstxout = ; every 10 ps nstvout = nstfout = nstxtcout = 250 nstenergy = 250 ; Bond parameters constraint_algorithm= lincs constraints = hbonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = System tau_t = 0.5 ref_t = 300 ; Pressure coupling is on Pcoupl = no pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on gen_vel = yes ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres Thanks Sanku -- 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] selecting res CYS from G53a5 using pdb2gmx
On 1/6/13 4:45 PM, Payman Pirzadeh wrote: Hi, I am using gromacs 4.5.4, and I am generating a topology file using G53a5 force field. My protein has a Cys residue which is supposed to be in thiolate state (negatively charged side chain). During issuing the pdb2gmx command I use the switch -inter to be prompted about the charge state of the ionisable side chains, but it asks nothing about Cys side chains except about they being involved in disulfide bonds. My questions are: 1. how can I get pdb2gmx ask me about the charge status of Cys residues? Or do I need to manually change their status in the topology file and output gro file (removing the HG)? 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, the total charge of the residue does not add to -1 but -0.5. Is anyone aware of any modifications to this force field parameters? I don't know of any. The AMBER force fields have parameters for the thiolate form of cysteine, but I've never seen them for Gromos96 force fields. That doesn't mean they don't exist, of course, but this is the sort of thing one should research prior to choosing a force field and then hoping for a solution later ;) -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] Calculating the helix moments
On 1/6/13 8:39 PM, 라지브간디 wrote: Dear users, I want to know how to calculate 1. The rotation angle of helix moments ? Probably g_principal does what you want. 2. number of water molecules interaction with ligand throughout the MD course ? g_mindist can calculate contacts between any groups you choose. -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] npt equilibrium
Dear Peter, Would you please let me know how much time approximately the system of protein/popc took to be npt-equilibrated sufficiently, in accordance with the simulation you have reported in Beyond modeling paper. In fact, I put the protein in popc and then ran NPT-equilibrium on it for 2 ns. When I go through the next step to run MD-run, I get error which indicates not sufficient equilibrated system. Thanks in advance. Sincerely, Shima -- 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] npt equilibrium
Dear Peter, Would you please let me know how much time approximately the system of protein/popc took to be npt-equilibrated sufficiently, in accordance with the simulation you have reported in Beyond modeling paper. In fact, I put the protein in popc and then ran NPT-equilibrium on it for 2 ns. When I go through the next step to run MD-run, I get error which indicates not sufficient equilibrated system. Thanks in advance. Sincerely, Shima -- 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 on GPU
Today I've tried to test gpu performance on the benchmark system ( explicit solvent with pme ) grompp-gpu -f md_sd.mdp -c conf -p topol.top -o md_test mdrun-gpu -device OpenMM:platform=Cuda,DeviceID=1,Memtest=15,force-device=no -v -deffnm md_test that produce the error Program mdrun-gpu, VERSION 4.5.5 Source code file: /home/own/gromacs_gpu/src/kernel/openmm_wrapper.cpp, line: 1365 Fatal error: OpenMM exception caught while initializating: cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors In the mailing list archive I've found the same error with the same card posted some time ago http://article.gmane.org/gmane.science.biology.gromacs.user/55577/match=openmm+exception+caught+while+initializating+cudaMemcpyToSymbol+setsim+copy+cSim+failed+invalid+device+symbol From that topic I've understood that 670 graphic card is not supported yet in Gromacs (4.55). I've checked the manual for the 4.6 beta version and does not found anything about supporting of that card in the lattest gromacs realeses as well. IS there any ways to solve that problem ? Could that error be linked with some others ? E.g I've installed nvidia drivers + cuda first and openMM 4.01 than. During gromacs compilation I've not forced with any errors. Thanks for help James 2013/1/6 Justin Lemkul jalem...@vt.edu: On 1/6/13 1:53 PM, James Starlight wrote: OK! I've compilated gromacs-gpu from the source using that tutorial for the Debian OS http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html The only thing that it lack is the installation mdrun_d-gpu but i'm not sure that double precission can be used with gpu. Could someone provide me with some tutorial which would show me basic mdrun options with the calculation on my gpu as well as some testing system? Everything you need to know (including benchmark systems) is posted at http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs. The invocation of mdrun-gpu is like any other mdrun, with GPU-specific information available by reading mdrun-gpu -h. -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 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
