Re: [gmx-users] random seed in molecular dynamics
hey thanks Mark What do you mean by -the random seed is in a different variable.Can you please explain the random seed On Fri, May 3, 2013 at 1:32 PM, Mark Abraham mark.j.abra...@gmail.comwrote: gen_vel controls the generation of random velocities. grompp follows it (but I'd have to check the code to see what it does if you use grompp -t). tprconv does not follow it. The random seed is in a different variable, but only does anything if gen_vel=yes. I am not sure what the basis of your confusion about repeated calls to grompp is. Mark On Fri, May 3, 2013 at 8:00 AM, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -thanks -- 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] Equilibrated system explodes after ~200ns?
Hi all, My simulation is composed of 2 protein chains wrapped around a lipid disk composed of a dozen different lipid types, water and ions in a 15nm cube. The protein encircles the mixed composition lipid disk. I've got 4 duplicate simulations with velocities generated from a different random seed. The starting structure for these simulations was taken from the end of a previous 200ns simulation (same settings but bigger box) which ended normally. I am using gromacs 4.6, with the gromos54a7 force field. No gpus. The first simulation exploded (a few atoms fly off into the distance leaving the rest intact) shortly before 150ns, two more have crashed shortly before 200ns. 1 is still running. Restarting a simulation has it crash at a different point. Over 3 steps of escalating LINCS warnings I get a warning followed by a fatal error The atoms initially involved in the LINCS warnings correspond to atoms around a double bond in a single lipid tail. Specifically in linoleic and linolenic (2 or 3 double bonds in sequence). The parameters used were adapted from the packaged POPC parameters using the same bond types from ffbonded.itp Energy graphs seem to indicate that the system is equilibrated. Does anyone have any ideas what's going on here? Thanks in advance, -Trayder P.S. mdp file -- View this message in context: http://gromacs.5086.x6.nabble.com/Equilibrated-system-explodes-after-200ns-tp5007963.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
Re: [gmx-users] constant protonation state MD
Then there is a wealth of papers that describe secondary structure determination from the experimental point of view that you should look for. NMR and CD would be the first obvious methods that come to mind, but there are probably others as well. These should be able to help you validate or invalidate your modeling observations. Best of luck! Jesper On May 5, 2013, at 9:47 PM, shahid nayeem msnay...@gmail.com wrote: It is a peptide. Shahid On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen jesoren...@ucsd.edu wrote: Shahid, This must be system dependent then because there are experimental methods, e.g. NMR and CD, that can help determine the secondary structure of proteins/peptides are various pH ranges. What is your system? A peptide? A globular protein? Best, Jesper On May 3, 2013, at 7:33 PM, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik and Baptista I am interested in simulating the change in secondary structure which is supposed to be influenced by the change in the pH environment of the cell. Experimentally it is not known but it has been proposed by many that the change in pH leads to change in conformation. I did constant protonation state MD at two different pH. I got an alpha helix converting to beta sheet at higher pH but not at lower pH. I am bothered to prove the reliability of the simulation results as experimentally it cant be established. Shahid On Sat, May 4, 2013 at 5:46 AM, bapti...@itqb.unl.pt wrote: Hi Shahid, As Erik said, it depends... on your system, on the process you are studying in that system, on the property you think it's relevant to study that process, etc. If your question refers to the (de)protonation of acidic and basic groups usually occuring in aqueous solution, there are methods to perform what is called constant-pH MD, where the protonation states of those groups change in a discrete or continuous way along the simulation. If you are interested, start with the corresponding GROMACS how-to ( http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation) and then search the literature. In any case, you don't need any of that fancy stuff unless you have reasons to think that the properties you want to study in your system are strongly dependent on protonation-conformation coupling effects. In some cases you may be suspicious about the effect of the protonation state of one group (e.g., a histidine), but that can be simply tested by performing two constant-protonation MD simulations, one for each state (you can even try to use a linear response approximation on top of that). But in most cases you don't need even that. For what it's worth: I was one of the first to develop and apply constant-pH MD and I don't bother to use it most of the time... :) Best, Antonio On Fri, 3 May 2013, Erik Marklund wrote: Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned
[gmx-users] correct traj for water/ions density
Dear All, I want to calculate water and ions density around polymer. After MD I see my polymer goes near the edges of box and rather some part is out of box. So in order to calculate water and ion density I think polymer should be near the center of box (please correct me if wrong) So by doing this: trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc mol -center Select group for centering: I selected my polymer only Select group for output: I selected all atoms (polymer + water + ions) Please let me know is this correct way of modifying trajectory to calculate water and ion density? regards, Jiom -- 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: correct traj for water/ions density
Sorry forgot to add::: by doing this I can see my polymer near the center of box On Mon, May 6, 2013 at 11:21 AM, gromacs query gromacsqu...@gmail.comwrote: Dear All, I want to calculate water and ions density around polymer. After MD I see my polymer goes near the edges of box and rather some part is out of box. So in order to calculate water and ion density I think polymer should be near the center of box (please correct me if wrong) So by doing this: trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc mol -center Select group for centering: I selected my polymer only Select group for output: I selected all atoms (polymer + water + ions) Please let me know is this correct way of modifying trajectory to calculate water and ion density? regards, Jiom -- 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] correct traj for water/ions density
On 5/6/13 4:21 AM, gromacs query wrote: Dear All, I want to calculate water and ions density around polymer. After MD I see my polymer goes near the edges of box and rather some part is out of box. So in order to calculate water and ion density I think polymer should be near the center of box (please correct me if wrong) What you are seeing is a completely normal consequence of periodic boundary conditions. You don't need to change the trajectory in any way to do density measurements; the resulting values will be the same before and after centering, since there is no outside or center of an infinite system. -Justin So by doing this: trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc mol -center Select group for centering: I selected my polymer only Select group for output: I selected all atoms (polymer + water + ions) Please let me know is this correct way of modifying trajectory to calculate water and ion density? regards, Jiom -- 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)
hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein -- regards M.SathishKumar -- 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 want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative . Can you please tell me making of disulphide as S- and S- is it correct and how to set force field to this. Thank you. -- regards M.SathishKumar -- 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)
I really don't think thats possible at the moment. All interactions in Reax, if I recall correctly, are dependent on bond order, which is not an implemented concept in gromacs. Erik On 6 May 2013, at 12:51, Sathish Kumar sathishk...@gmail.com wrote: hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein -- regards M.SathishKumar -- 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] Reax force field
On 5/6/13 6:51 AM, Sathish Kumar wrote: hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein It won't be easy to use Reax, if it's even possible. You would have to make some serious code modifications, both in terms of energy calculations and topology interpretation. The former could possibly be achieved with tabulated potentials, but the latter would certainly have to be coded. Reax doesn't use traditional bonds, and the Gromacs topology format doesn't know how to deal with bond orders in lieu of actual bonds. -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] Thiolate cysteine
On 5/6/13 7:03 AM, Sathish Kumar wrote: I want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative . Can you please tell me making of disulphide as S- and S- is it correct and how to set force field to this. Some force fields (like the Amber parameter sets and some others) have the CYM residue, which is the thiolate form of cysteine. Find which force fields have this residue, read about their use, and make a choice based on what you find. -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] correct traj for water/ions density
Dear Justin, You don't need to change the trajectory in any way to do density measurements I read sometime before in some paper: water density falls around polymer (COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume the polymer must be near the center of box so 5nm on either sides. Then in my case (polymer at the box edge) how the box size will be considered. I mean to say if my box is 10x10x10 and I calculate density it will never fall around 5nm distance from polymer as my polymer is at edge and will give different pattern. regards, On Mon, May 6, 2013 at 1:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/13 4:21 AM, gromacs query wrote: Dear All, I want to calculate water and ions density around polymer. After MD I see my polymer goes near the edges of box and rather some part is out of box. So in order to calculate water and ion density I think polymer should be near the center of box (please correct me if wrong) What you are seeing is a completely normal consequence of periodic boundary conditions. You don't need to change the trajectory in any way to do density measurements; the resulting values will be the same before and after centering, since there is no outside or center of an infinite system. -Justin So by doing this: trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc mol -center Select group for centering: I selected my polymer only Select group for output: I selected all atoms (polymer + water + ions) Please let me know is this correct way of modifying trajectory to calculate water and ion density? regards, Jiom -- ==**== 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] Thiolate cysteine
Thank you sir On Mon, May 6, 2013 at 4:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/13 7:03 AM, Sathish Kumar wrote: I want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative . Can you please tell me making of disulphide as S- and S- is it correct and how to set force field to this. Some force fields (like the Amber parameter sets and some others) have the CYM residue, which is the thiolate form of cysteine. Find which force fields have this residue, read about their use, and make a choice based on what you find. -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 -- regards M.SathishKumar -- 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] Reax force field
Thank you sir On Mon, May 6, 2013 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/13 6:51 AM, Sathish Kumar wrote: hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein It won't be easy to use Reax, if it's even possible. You would have to make some serious code modifications, both in terms of energy calculations and topology interpretation. The former could possibly be achieved with tabulated potentials, but the latter would certainly have to be coded. Reax doesn't use traditional bonds, and the Gromacs topology format doesn't know how to deal with bond orders in lieu of actual bonds. -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 -- regards M.SathishKumar -- 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 want to do simulation of protein at pH 12 so i have to deprotanate tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx command -- regards M.SathishKumar -- 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] correct traj for water/ions density
On 5/6/13 7:32 AM, gromacs query wrote: Dear Justin, You don't need to change the trajectory in any way to do density measurements I read sometime before in some paper: water density falls around polymer (COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume the polymer must be near the center of box so 5nm on either sides. Then in my case (polymer at the box edge) how the box size will be considered. I mean to say if my box is 10x10x10 and I calculate density it will never fall around 5nm distance from polymer as my polymer is at edge and will give different pattern. Now the statement of your problem is more clear. To calculate the density within the box, you do not need to do any manipulation. For your purpose, where a fixed reference is convenient, there's certainly nothing wrong with centering the polymer. -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] Tryptophan and tyrosine protonation
Please use informative subject lines. No subject often gets flagged as spam, and thus people who may be able to help you may never see your message. On 5/6/13 7:58 AM, Sathish Kumar wrote: I want to do simulation of protein at pH 12 so i have to deprotanate tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx command The answer is the same as with cysteine - either the force field will have parameters for such species or it won't. If it doesn't, you have to implement suitable parameters; there is no magic that pdb2gmx can do for you. Anionic tyrosine is more likely to have parameters available somewhere. I have never heard of the tryptophan side chain being deprotonated under any conditions. -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] Can Gromacs do oscillatory shear?
Hi all, I am trying to preform oscillatory shear flow on Gromacs. Is there any existing commands/codes to do it or do I have to modify the code myself? If I have to modify code, where can I find the source code for deform? Thank you so much! Shirley Young -- 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] Still having issues analyzing normal-mode hessian
Hello, I have successfully generated a 945MB mtx hessian storing the normal modes of a ~1500AA protein using mdrun with the nm integrator and no cutoffs. However, when I try to analyze the normal modes and create trajectories using g_nmeig, I can't seem to generate any output. I am running g_nmeig_mpi_d with the following options: mpiexec_mpt g_nmeig_mpi_d -f input.mtx -s NMA.tpr -of NMA_freq.xvg -ol NMA_val.xvg -v NMA_vec.trr and have been letting it run a few times for up to 5 days on 128 Itanium nodes with 120gb maximum memory. When the job finally aborts after running out of cpu time, I get a standard output file that's about 8GB (which I am unable to open). Is there a way to force g_nmeig to generate some output or at least show me what is going on? Am I running it with the correct options? There isn't a lot of documentation on these normal-mode specific programs so I don't know how to begin troubleshooting. Thanks, *Bryan Roessler | Graduate Research Assistant* UAB | The University of Alabama at Birmingham *uab.edu/cmdb* Knowledge that will change your world -- 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] Still having issues analyzing normal-mode hessian
On 5/6/13 2:16 PM, Bryan Roessler wrote: Hello, I have successfully generated a 945MB mtx hessian storing the normal modes of a ~1500AA protein using mdrun with the nm integrator and no cutoffs. However, when I try to analyze the normal modes and create trajectories using g_nmeig, I can't seem to generate any output. I am running g_nmeig_mpi_d with the following options: mpiexec_mpt g_nmeig_mpi_d -f input.mtx -s NMA.tpr -of NMA_freq.xvg -ol NMA_val.xvg -v NMA_vec.trr and There is no point in trying to run in parallel; only mdrun is parallelized. That could be one source of problem. have been letting it run a few times for up to 5 days on 128 Itanium nodes with 120gb maximum memory. When the job finally aborts after running out of cpu time, I get a standard output file that's about 8GB (which I am unable to open). Is there a way to force g_nmeig to generate some output or at least show me what is going on? Am I running it with the correct options? There isn't a lot of documentation on these normal-mode specific programs so I don't know how to begin troubleshooting. Run interactively and try with a smaller data set, something that will consume very little memory, then scale up. -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] REMD Statistics
On Mon, May 6, 2013 at 3:48 AM, Kong xq xqkong...@gmail.com wrote: Hi Mark, Thanks for your great help. I am sorry for the negligence to state the variation value correctly( it should be 0.011 rather than 0.11). Does this somewhat small value indicate the generalized equilibrium achieved? It might be consistent with it, but it is never diagnostic of it. FWIW, I have never seen an REMD study that attempted to address whether generalized equilibrium was achieved. I will search the papers you suggested. I am wondering whether the histogram is the gold standard for effectively constructing REMD flow. Moreover, how to do the potential energy overlap analysis in Gromacs, from the edr file for each replica ？Does any tool avalible in Gromacs to do this job ? g_energy to get the data for each replica, then your favorite analysis package to form histograms, and graphing program to overlay the plots. The histograms can be done with g_analyze. 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
[gmx-users] About Potential energy calculation
Hi all I am doing an NVE simulation of a protein immersed in water, and I want to keep track of the potential energy in the protein. Do you know how can I do it?. I tried saving the energy of the protein ( the protein as an energy group) in the .edr file, but when I checked the file with g_energy, it does not give me the option of potential energy only for the protein, it gives me the total potential energy. I really appreciate your help. John M. Espinosa Duran PhD student of Chemical Physics Indiana University -- 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 Potential energy calculation
On 5/6/13 5:58 PM, jhon michael espinosa duran wrote: Hi all I am doing an NVE simulation of a protein immersed in water, and I want to keep track of the potential energy in the protein. Do you know how can I do it?. I tried saving the energy of the protein ( the protein as an energy group) in the .edr file, but when I checked the file with g_energy, it does not give me the option of potential energy only for the protein, it gives me the total potential energy. The potential energy of a subset of atoms is not stored in the .edr file; only short-range nonbonded interactions can be decomposed by using energygrps. There are a variety of reasons for doing so. The easiest way to get the quantity you want is to use tpbconv create a .tpr file that contains only the protein and then re-calculate energies using mdrun -rerun on the existing trajectory. -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] Re: About Potential energy calculation
Hi Justin Thanks for your answer. Actually, you are right and that is what I am doing now, but it is really time consuming and it is like double calculating because the potential energy is computed during the MD. Any way thanks John Michael -- View this message in context: http://gromacs.5086.x6.nabble.com/About-Potential-energy-calculation-tp5007982p5007984.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
Re: [gmx-users] Proteins with ADP ATP cofactors
Dear Stephan, thank you for your reply. I'm performing some test with antechamber for a de-novo parametrization, hope to see some good results with it. You probably have to do a hand job. Look at the .itp/top files and then the force field parmeters, here's not many atoms, so it would take only a couple hours. -- 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: keeping water (entirely) out of the bilayer core
Chris, not entirely sure if would work, but what about set of particles located
at the center of the bilayer (might require anchoring/freezing) which only
interacts (via repulsion only) with water, and setting the interaction such
that it manages to exclude it from the bilayer region you require.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] On Behalf Of Christopher Neale
Sent: Saturday, 4 May 2013 10:46 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] keeping water (entirely) out of the bilayer core
Dear users:
I am interested in running simulations of lipid bilayers in which I
keep all water molecules out of the bilayer core
(not just statistically, but absolutely). However, I have been unable
to figure out how to do it.
I'll list what I have tried in the hope that others have some ideas or
even perhaps know how to do this
with standard gromacs.
Everything that I have tried revolves around using the pull code,
setting the entire lipid bilayer as the reference
group, and having thousands of pulled groups -- one for each water
molecule. Also, I modified the gromacs
source code in mdlib/pull.c (version 4.6.1) so that the force is only
applied when the displacement is smaller than
the desired distance and not when the displacement is larger than the
specified distance (to keep water out but
then to otherwise let it go anywhere without bias):
static void do_pull_pot(int ePull,
t_pull *pull, t_pbc *pbc, double t, real
lambda,
real *V, tensor vir, real *dVdl)
{
intg, j, m;
dvec dev;
double ndr, invdr;
real k, dkdl;
t_pullgrp *pgrp;
/* loop over the groups that are being pulled */
*V= 0;
*dVdl = 0;
for (g = 1; g 1+pull-ngrp; g++)
{
pgrp = pull-grp[g];
get_pullgrp_distance(pull, pbc, g, t, pgrp-dr, dev);
/* ## HERE IS THE CODE CHANGE
if(dev[0]0.0){
dev[0]=0.0;
}
/* End code snippit */
The most relevant lines from the .mdp file were:
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start = no
pull_ngroups = 9000
pull_group0 = POPC
pull_group1 = r_1__OW
pull_init1 = 1.9
pull_k1 = 500
pull_group2 = r_2__OW
pull_init2 = 1.9
pull_k2 = 500
... etc...
The problem with this was that it crashed immediately with an error
that my pulling distance was
greater than 1/2 of the box vector.:
Fatal error:
Distance of pull group 165 (5.353939 nm) is larger than 0.49 times the
box size (5.395960)
Pretty obvious in retrospect. If I could get this error to go away,
then everything should be fine because I have modified the code so that
forces are zero at large displacements. However, I am worried that if I
simply modify grompp to bypass this error then I might get some type of
strange and possibly silent error in mdrun. Any thoughts on this are
really appreciated.
For my second try, I used pull_geometry = direction-periodic (see more
details below), but that also didn't work
because if I set pull_vec1 = 0 0 1, then everything gets pulled to the
upper part of the box (and LINCS errors
ensue), rather than simply pulling away from the bilayer.
Pcoupl= berendsen
pcoupltype = semiisotropic
compressibility= 4.5e-5 0
pull = umbrella
pull_geometry= direction-periodic
pull_start = no
pull_ngroups = 9000
pull_group0 = POPC
pull_group1 = r_1__OW
pull_init1 = 1.9
pull_k1 = 500
pull_vec1= 0 0 1
pull_group2 = r_2__OW
pull_init2 = 1.9
pull_k2 = 500
pull_vec2= 0 0 1
... etc...
If anybody has an idea about how I could get this to work with standard
gromacs or with a modified version, I would be very grateful to hear
your thoughts.
Thank you,
Chris.
--
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[gmx-users] mdrun-gpu error message on Gromacs 4.5.5
Hi, I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM). This is my first time using a GPU. I get the following error message when attempting to run mdrun-gpu with my .tpr file: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /usr/local/src/gromacs-4.5.5/src/kernel/openmm_wrapper.cpp, line: 1365 Fatal error: OpenMM exception caught while initializating: getPropertyValue: Illegal property name For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I get this error when calling with: mdrun-gpu -s topol.tpr and with: mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no -s topol.tpr I can't seem to find this particular error message in the documentation or previously discussed on this mailing list. Does this error message suggest that I am calling mdrun-gpu incorrectly, or that OpenMM is improperly installed? Thank you kindly for your time! Andrew DeYoung Carnegie Mellon University -- 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] keeping water (entirely) out of the bilayer core
Hi Chris, Just think of another possible way without modifying the code. The task can be achieved by increasing the LJ repulsion term between the lipid tail atoms and water molecules, but keeping all other interactions unchanged. To do so, the free energy code can be used. You can create a state_B, at which only the LJ repulsion term between the lipid tail atoms and water molecules is rescaled, other interactions are the same as state_A, and then run the simulations at lambda=1. Jianguo From: Christopher Neale chris.ne...@mail.utoronto.ca To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Monday, 6 May 2013, 2:46 Subject: [gmx-users] keeping water (entirely) out of the bilayer core Thank you for the advice Jianguo. This seems like a good way forward. I was hoping not to have to learn how to use new software, but perhaps it is time. Thank you, Chris. -- original message -- Hi Chris, Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective variable as mindist between the water molecules and the lipid tails. And then apply wall potential to keep this CV above a certain value. Jianguo Dear users: I am interested in running simulations of lipid bilayers in which I keep all water molecules out of the bilayer core(not just statistically, but absolutely). However, I have been unable to figure out how to do it. I'll list what I have tried in the hope that others have some ideas or even perhaps know how to do this with standard gromacs. ... -- 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] center of mass and box co-ordinates
Hello Justin sir In your tutorial file for umbrella sampling for Aβ42 protofibril, what was the criteria used to determine the coordinates of center of mass and box size which you have takes as editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12 -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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
