[gmx-users] MD stop,systme not equilibrium
Dear, when i make MD of my system, i set the MD stop ater 3ns. however, when the gromacs stop , i find that the system of protein and ligand is not equilibrium, i want to continue the process to 5ns. but i don't konw how to do this.please help me. thank you very much! -- 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] Fwd: clustering based on side-chain conformations
Dear Justin, Thanks for your immediate reply. Is it possible to do clustering based on side-chain RMSF in gromacs? What about dihedral angle order parameters in gromacs?. Does it provide any information about what I want to know? Thanking you once again regards Anu On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 1, 2013 at 4:52 AM, anu chandra anu80...@gmail.com wrote: Dear amber users, I am working with protein-ligand interaction. The protein shows high degree of side-chain conformational changes and minimal backbone conformational changes during ligand binding. In order to capture these side chain flexibility, as a initial step, I would like to do clustering based on the side-chain flexibility (i.e. categorise different areas in protein based on the degree of side chain flexibility). Is there a way to do such a calculation in Gromacs?. Can any one suggested me a way to proceed with this sort of analysis? g_cluster does RMSD-based clustering. That's not flexibility per se, but might be informative. If you do fitting based on side chains (which might be difficult, since side chains flop around a lot), that's about as close to achieving what you're after as I can think of using standard Gromacs programs. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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 4.6.1 on win7?
IIRC, the default Cygwin gcc is too old to compile GROMACS, as discussed on this list in the last few months some time. I don't know how easy it is to get a new one via the Cygwin package system. Mark On Mon, Apr 1, 2013 at 5:03 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 1, 2013 at 8:58 AM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx, I tried to install 4.6.1 version through cygwin and got following error by using this command : CMake Error at CMakeLists.txt:811 (message): Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler. When I use SSE4.1 i got this error : CMake Error at CMakeLists.txt:750 (message): Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support. Please need an guidance to install it. Thanks. What compiler (and version) are you using? Apparently whatever is installed does not support the features that Gromacs thinks you should have available. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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
Fw: Aw: Re: [gmx-users] Re: density profile
Sorry, meant to post this on the bb. Gesendet:Dienstag, 02. April 2013 um 11:50 Uhr Von:lloyd riggs lloyd.ri...@gmx.ch An:vvcha...@gmail.com Betreff:Aw: Re: [gmx-users] Re: density profile How would you set up a gas/gas interface, say modeled after a large gas planet or upper atmosphere, without effects from garvity and pressures in the 10K plus ATM? In such a system the gases behave almost like liquids, but most effects are from extreems of conditions. Actaul interfaces though I assume would include large amounts of mixing right at the atomic level interface, but I have no clue how far this would extend. If you remove rotational effects, I am willing to bet you can model a gas/gas interface at the atomic level with extreem conditions, which might be an aset in some fileds/areas of research. Minus gravitational effects though, I do not know if they could work properly. You can however set up a ligid gas interface by introducing box systems with differences in force at a plain across the midpoint equal to gas/liquid interfaces, or gradients of force, etc...but in all cases I assume a minimal amount of programming might be necessary. Opinions/answers anyone? Stephan Watkins Gesendet:Montag, 01. April 2013 um 20:43 Uhr Von:Dr. Vitaly Chaban vvcha...@gmail.com An:Elisabeth katesed...@gmail.com, gmx-users@gromacs.org Betreff:Re: [gmx-users] Re: density profile There is a wonderful data page devoted to methane in wikipedia... It follows from this webpage that you will get a perfect density profile if you decrease your T down to 150K... On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth katesed...@gmail.com wrote: You are right. I compressed my alkane system under NPT at 400 K at 100 bar. The normal boiling point is below 425 K. So it seems there in no way one can obtain profiles obove boiling point of liquid given than with the current NVT recipe molecules tend to fill up the free zone no matter how much pressure was applied in the previous NPT runs? You cannot get a profile just because you have NO LIQUID and NO INTERFACE upon these conditions. Gas fills all the available space, there is no such thing as gas/gas interface. And yeah... Forget about NPT and learn the Gibbs phase rule. Dr. Vitaly Chaban On 1 April 2013 14:22, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.com wrote: Hi Vitaly, The problem was with cpt file since it re sets the last line of gro. I removed the -f flag and now the Z direction is extended. However, I see that molecules tend to fill up the upper zone (free space) rapidly. I am wondering how I can obtain the density profile if I am going to get another uniformly distributed box after this NVT run? Here we come to the question what your system is composed of... Based on the density profile, this is not a (conventional) liquid... Polymer, non-Newtonian liquid ... or what? If molecules tend to fill vacuum, it can only mean that the matter you are simulating is above critical point. What is your T and what are the particles in your box? Dr. Vitaly Chaban I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: I think if you use checkpoint files, the program does not read either MDP, or GRO, or TOP, or anything except CPT. Dr. Vitaly Chaban On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth katesed...@gmail.comwrote: Hi vitaly, The initial structure is indeed extended but the final output.gro is not. I think its because I am using the cpt file from the previous NPT runs as input for the new runs? Do I have to remove the -t flag? On 1 April 2013 12:47, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Hi Elisabeth - The only explanation is that you actually DID NOT extend the box in Z direction. Look at the last line of confout.gro. g_density -d Z gives you a [local] density versus Z coordinate. Dr. Vitaly Chaban On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth katesed...@gmail.comwrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Maximum force on atom and unpacked lipids
Dear Users, I have inserted protein and carbohydrate in DPPC membrane according to the KALP tutorials. After inserting both molecules, I checked by using VMD, the atoms around my protein and ligand were overlapped. But I applied position restraints to protein and ligand and run Inflategro scripts for shrinking and packing. Perl inflategro result There are 3 lipids within cut-off range... 1 will be removed from the upper leaflet... 2 will be removed from the lower leaflet... Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 1147 Protein Y-min/max: 1945 X-range: 36 AY-range: 26 A Building 36 X 26 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 7.5 nm^2 Area per lipid: 10.4673818624 nm^2 Area per protein, upper half: 5.5 nm^2 Area per lipid, upper leaflet : 10.4160534349206 nm^2 Area per protein, lower half: 4.25 nm^2 Area per lipid, lower leaflet : 10.6042155870968 nm^2 Writing Area per lipid... Done! ___ 1st EM result _ --- --- Step= 576, Dmax= 8.0e-03 nm, Epot= -9.29249e+04 Fmax= 5.95606e+03, atom= 504 Step= 578, Dmax= 4.8e-03 nm, Epot= -9.29638e+04 Fmax= 8.42117e+02, atom= 504 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 579 steps Potential Energy = -9.2963797e+04 Maximum force = 8.4211664e+02 on atom 504 Norm of force = 4.9797871e+01 Then in EM step, showing Maximum force on certain atom. I performed shrinking step until it converged. But every EM I have Max Force on selected atom. The final complex still have unpacked lipids. How to correct this or whether will be corrected during Equilibration steps. I think the problem lies in the Ist EM step itself. Kindly give some suggestions Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/Maximum-force-on-atom-and-unpacked-lipids-tp5006817.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] Position restraints
Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've started both dynamics with/without posrestraints on my residue, however I'm really not sure that my results from both of them are different. But I want to do everything in right way, so what can you say about this? Thank you -- * Nemo me impune lacessit* -- 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] MD stop,systme not equilibrium
On 4/2/13 3:24 AM, aixintiankong wrote: Dear, when i make MD of my system, i set the MD stop ater 3ns. however, when the gromacs stop , i find that the system of protein and ligand is not equilibrium, i want to continue the process to 5ns. but i don't konw how to do this.please help me. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -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] Fwd: clustering based on side-chain conformations
On 4/2/13 4:58 AM, anu chandra wrote: Dear Justin, Thanks for your immediate reply. Is it possible to do clustering based on side-chain RMSF in gromacs? Not that I'm aware of. What about dihedral angle order parameters in gromacs?. Does it provide any information about what I want to know? You can probably get some useful information, but I don't know how to calculate such quantities in Gromacs, and any clustering you would do would have to be external to Gromacs. -Justin Thanking you once again regards Anu On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 1, 2013 at 4:52 AM, anu chandra anu80...@gmail.com wrote: Dear amber users, I am working with protein-ligand interaction. The protein shows high degree of side-chain conformational changes and minimal backbone conformational changes during ligand binding. In order to capture these side chain flexibility, as a initial step, I would like to do clustering based on the side-chain flexibility (i.e. categorise different areas in protein based on the degree of side chain flexibility). Is there a way to do such a calculation in Gromacs?. Can any one suggested me a way to proceed with this sort of analysis? g_cluster does RMSD-based clustering. That's not flexibility per se, but might be informative. If you do fitting based on side chains (which might be difficult, since side chains flop around a lot), that's about as close to achieving what you're after as I can think of using standard Gromacs programs. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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 -- 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] Maximum force on atom and unpacked lipids
On 4/2/13 5:56 AM, sdshine wrote: Dear Users, I have inserted protein and carbohydrate in DPPC membrane according to the KALP tutorials. After inserting both molecules, I checked by using VMD, the atoms around my protein and ligand were overlapped. But I applied position restraints to protein and ligand and run Inflategro scripts for shrinking and packing. Perl inflategro result There are 3 lipids within cut-off range... 1 will be removed from the upper leaflet... 2 will be removed from the lower leaflet... Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 1147 Protein Y-min/max: 1945 X-range: 36 AY-range: 26 A Building 36 X 26 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 7.5 nm^2 Area per lipid: 10.4673818624 nm^2 Area per protein, upper half: 5.5 nm^2 Area per lipid, upper leaflet : 10.4160534349206 nm^2 Area per protein, lower half: 4.25 nm^2 Area per lipid, lower leaflet : 10.6042155870968 nm^2 Writing Area per lipid... Done! ___ 1st EM result _ --- --- Step= 576, Dmax= 8.0e-03 nm, Epot= -9.29249e+04 Fmax= 5.95606e+03, atom= 504 Step= 578, Dmax= 4.8e-03 nm, Epot= -9.29638e+04 Fmax= 8.42117e+02, atom= 504 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 579 steps Potential Energy = -9.2963797e+04 Maximum force = 8.4211664e+02 on atom 504 Norm of force = 4.9797871e+01 Then in EM step, showing Maximum force on certain atom. I performed shrinking step until it converged. But every EM I have Max Force on selected atom. There will always be some atom with a maximum force; that's how EM works. As long as that maximum force is below an acceptable tolerance, there is no problem. The final complex still have unpacked lipids. This statement doesn't make much sense to me. Either InflateGRO worked, or it didn't. There shouldn't be any halfway. How to correct this or whether will be corrected during Equilibration steps. I think the problem lies in the Ist EM step itself. Kindly give some suggestions I don't see evidence of a problem, and certainly not within the first EM step. -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] Position restraints
On 4/2/13 6:07 AM, alex rayevsky wrote: Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've started both dynamics with/without posrestraints on my residue, however I'm really not sure that my results from both of them are different. But I want to do everything in right way, so what can you say about this? Restraints during equilibration are used to prevent unnatural forces from the unequilibrated solvent and help prevent deformation of the structure. It's never a bad idea to restrain the whole solute. If I were reading a paper that described restraining the whole solute, except for one residue because it was special or difficult to deal with, I would immediately be suspicious. -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
Good News for Cygwin users (was: Re: [gmx-users] gromacs 4.6.1 on win7?)
On 01.04.2013 14:58, 라지브간디 wrote: I tried to install 4.6.1 version through cygwin and got following error by using this command : In the last weeks of March 2013, there has been significant progress made on the cygwin packages. Since April, 1st, there is even a 64-bit build including gcc 4.8 (!) available. ftp://ftp.gwdg.de/pub/linux/sources.redhat.com/cygwin/64bit/ (other mirrors: http://cygwin.com/mirrors.html) On the usual 32-bit build, the gcc 4.7.2, which compiles gromacs fine, is available since mid-March. You can choose from gcc 4.3.x, 4.5.x, and 4.7.2 under gcc-4. If I get some time left, I'll test the 64-bit gcc-4.8 system and report back. Regards M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD general protocol ...
Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. I will be very grateful to you for your help and suggestion. With Best Regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD general protocol ...
On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -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 general protocol ...
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? Erik -- 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
[gmx-users] Re: Salt bridge Calculations
Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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 general protocol ...
I would look on some paper which temperature ranges and conditions (NPT/NVT) were used for systems of a similar size and with a similar aim. 2013/4/2 rama david ramadavidgr...@gmail.com Dear friends , Thank you justin and Mark for your suggestion I increases my temp range from 310-360 K Now I get 20 replicas . Is in such large temp range wlll it be good to use NPT. Would you tell me the temp differences in which box instability generally arises .. Is my working-flow right or need to change much Thank you With Best Regards.. On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? Erik -- 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 -- 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] REMD general protocol ...
Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your suggestion. On Tue, Apr 2, 2013 at 6:45 PM, massimo sandal deviceran...@gmail.comwrote: I would look on some paper which temperature ranges and conditions (NPT/NVT) were used for systems of a similar size and with a similar aim. 2013/4/2 rama david ramadavidgr...@gmail.com Dear friends , Thank you justin and Mark for your suggestion I increases my temp range from 310-360 K Now I get 20 replicas . Is in such large temp range wlll it be good to use NPT. Would you tell me the temp differences in which box instability generally arises .. Is my working-flow right or need to change much Thank you With Best Regards.. On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? Erik -- 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 -- 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
[gmx-users] install gromacs 4.5.5 on cluster
hello gromacs users, I was trying to install gromacs 4.5.5 on the cluster. the cluster info: uname -a Linux mgr.itp 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux I have successfully installed fftw3 and gsl on it. then I try to install the Gromacs 4.5.5 with the following commad: export CPPFLAGS=-I$HOME/Software/gsl-1.13/include/gsl -I$HOME/Software/fftw-3.2.2/include -I/opt/vltmpi/OPENIB/mpi.icc.rsh/include export LDFLAGS=-L$HOME/Software/gsl-1.13/lib -L$HOME/Software/fftw-3.2.2/lib -L/opt/vltmpi/OPENIB/mpi.icc.rsh/lib ./configure --prefix=$HOME/Software --enable-mpi --with-fft=fftw3 --with-gsl --enable-double --program-suffix=_mpi no problem until here. then: make error came up like this: /usr/include/md5.h(27): error: identifier UINT4 is undefined UINT4 state[4]; /* state (ABCD) */ ^ /usr/include/md5.h(28): error: identifier UINT4 is undefined UINT4 count[2];/* number of bits, modulo 2^64 (lsb first) */ ^ . Does anyone know how to solve this problem? By the I have tried install on my personal computer with the same command,it's succeed. Richor -- 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: Salt bridge Calculations
You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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] 4.6.1 support double precision GPU now?
Hello: I am wondering is double precision supported in current 4.6.1 GPU version? Otherwise it would be very slow to use CPU version running free energy calculations thank you very much best Albert -- 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] 4.6.1 support double precision GPU now?
On Apr 2, 2013, at 5:47 PM, Albert mailmd2...@gmail.com wrote: Hello: I am wondering is double precision supported in current 4.6.1 GPU version? Otherwise it would be very slow to use CPU version running free energy calculations…. Hi Albert, no, GPU calculations can be done only in single precision. Best, Carsten thank you very much best Albert -- 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] g_density: Segmentation fault
Dear all, I am trying to get the density profile for my liquid-vacuum interface using g_density -f trr -s tpr however g_density gives Segmentation fault. Does anyone had clue what could be wrong? Please comment, Thanks. Group 0 ( System) has XXX elements Group 1 ( Other) has XXX elements Select a group: 0 Selected 0: 'System' trn version: GMX_trn_file (single precision) Last frame 10 time 1.000 Segmentation fault -- 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: Salt bridge Calculations
Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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] REMD general protocol ...
On 4/2/13 7:38 AM, Erik Marklund wrote: On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? I suppose, but then why bother with the exchange overhead? Seems to me that if you're only interested in temperature-dependent quantities, you can do that with independent simulations at different temperatures. -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 general protocol ...
On 4/2/13 9:24 AM, rama david wrote: Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your suggestion. The best training experience would be to take a simple example from the literature and reproduce it. It is very hard to try to teach someone completely via email, especially since we do not know the scope and goals of what you are doing. With respect to the question about pressure coupling stability over 310 - 360 K, I don't know offhand what to expect, but in general, I think this is a standard limitation within REMD and you'll probably encounter it. Again, find a protocol for a similar system and try to get things working. It will be easier to help you if you have a known objective that has been demonstrated to work. -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: Salt bridge Calculations
On 4/2/13 11:58 AM, Kavyashree M wrote: Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Does this really give you any useful information? You'll get an output file with putative contacts derived from an arbitrary cutoff for any possible positive-negative pair defined in the index group. I think the g_dist approach is far more useful and gives you exact insight into specific pairs. It takes a bit more prep work, but looping the calculations is trivial to do to make them efficient. -Justin Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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 -- 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] g_density: Segmentation fault
On 4/2/13 11:57 AM, Elisabeth wrote: Dear all, I am trying to get the density profile for my liquid-vacuum interface using g_density -f trr -s tpr however g_density gives Segmentation fault. Does anyone had clue what could be wrong? Please comment, Thanks. Group 0 ( System) has XXX elements Group 1 ( Other) has XXX elements Select a group: 0 Selected 0: 'System' trn version: GMX_trn_file (single precision) Last frame 10 time 1.000 Segmentation fault Segmentation faults are generic memory errors. Without a debugging backtrace, there's very little to suggest. -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: Hamiltonian replica exchange umbrella sampling with gmx 4.6
Hi Michael,
Do the codes now support walking in multidimensional parameter space? i.e.,
a state is defined by a set of lambda parameters {l1,l2,l3,...,ln} and a MC
move is attempted along one of the parameter, which is randomly picked.
Thanks,
Dejun
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Re: [gmx-users] g_density: Segmentation fault
Hi Justin, Do I have to read less frames to circumvent the problem? I know g_density has been used for this purpose so there should be a way to resolve this. I am reading 1000 frames... Thanks On 2 April 2013 12:40, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 11:57 AM, Elisabeth wrote: Dear all, I am trying to get the density profile for my liquid-vacuum interface using g_density -f trr -s tpr however g_density gives Segmentation fault. Does anyone had clue what could be wrong? Please comment, Thanks. Group 0 ( System) has XXX elements Group 1 ( Other) has XXX elements Select a group: 0 Selected 0: 'System' trn version: GMX_trn_file (single precision) Last frame 10 time 1.000 Segmentation fault Segmentation faults are generic memory errors. Without a debugging backtrace, there's very little to suggest. -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] REMD general protocol ...
Thank you justin. I will do the same. On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 9:24 AM, rama david wrote: Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your suggestion. The best training experience would be to take a simple example from the literature and reproduce it. It is very hard to try to teach someone completely via email, especially since we do not know the scope and goals of what you are doing. With respect to the question about pressure coupling stability over 310 - 360 K, I don't know offhand what to expect, but in general, I think this is a standard limitation within REMD and you'll probably encounter it. Again, find a protocol for a similar system and try to get things working. It will be easier to help you if you have a known objective that has been demonstrated to work. -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] Free webinar on Gromacs-4.6 and GPUs together with Nvidia
Hi again! Just a quick update - we've had lots of interest for the webinar this thursday (which is great!). We're pretty close to breaking their all-time record for webinars, and you still have two days to sign up, so hopefully we'll do it ;-) I will try to answer as many Gromacs/GPU-related questions as we have time for during the event, but Nvidia has also promised to try and record all questions they get, and we'll try to answer the ones we don't have time for later in a GPU-FAQ on our website. So, this might be a good point to think about things you want to ask! Cheers, Erik On Mar 20, 2013, at 5:14 PM, Erik Lindahl lind...@cbr.su.se wrote: Hi, On April 4 (9-10am, US pacific time), Nvidia is helping us organize a web seminar about Gromacs-4.6 and all the new GPU capabilities. While I would expect their representative to spend a couple of minutes talking about hardware, they will invite interested users to free remote testdrives of Gromacs running on their hardware, and I hope it goes without saying that I will cover Gromacs-GPU from the scientific side, what it can do for your simulations, how to use it most efficiently, and what hardware we are using ourselves for it! However, there is one caveat - since this is run on the web with possibilities to ask questions, etc., you will need to register here (feel free to spread the link): https://www2.gotomeeting.com/register/802328986 All the best, Erik-- 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: Hamiltonian replica exchange umbrella sampling with gmx 4.6
Hi, Dejun-
Right now, the vector of lambda parameters is simply vdw, coul, bonded,
restraint, temperature. You can't have, say, 2 different coul vectors or
two different restraint vectors for different restraints. But you can
change any of these components.
You define the vector manually by writing out the list. So to do 2D in vdw
and restraints, you would define states:
vdw-lambdas= 0.0 0.0 0.0 0.5 0.5 0.5 1.0 1.0 1.0
restraint-lambdas = 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0
Multidimensional movement in parameter space with replica exchange can be
done with the md setting '-nex Nswaps'. This does multiple pair swaps,
instead of just neighbor pair swaps. I'd suggest something like Nswaps =
N^3, where N is the number of lambda states. This is a close approximation
to Gibbs sampling (http://jcp.aip.org/resource/1/jcpsa6/v135/i19/p194110_s1),
where _all_ permutations are selected based on their Boltzmann weight.
It's an approximation because with a finite number of swaps, you don't
quite get uncorrelated moves in state space, but it is rigorously correct
thermodynamically. It is more powerful than randomly selecting a dimension
to move in, since it allows moves in all dimensions simultaneously with
proper weight.
Note that the number of lambdas states is hardcoded as 1024, but that can
(I think) be edited as desired without causing direct problems (other than
perhaps needing to make the .mdp lines longer).
We are working on more general multistate lambda vector formalism for 5.0.
If you have suggestions, let me know.
I'd be happy to look over input files or give additional advice on a
specific setup.
On Tue, Apr 2, 2013 at 12:52 PM, Dejun Lin dejun@gmail.com wrote:
Hi Michael,
Do the codes now support walking in multidimensional parameter space? i.e.,
a state is defined by a set of lambda parameters {l1,l2,l3,...,ln} and a MC
move is attempted along one of the parameter, which is randomly picked.
Thanks,
Dejun
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Re: [gmx-users] Re: Salt bridge Calculations
Sir, This g_hbond will generate a matrix similar to what g_saltbr would have given in terms of variation of distance between two charge groups. I want to find out the variation of all the salt bridges in the protein over the trajectory, if I have to use g_dist with an index of positive atoms and another of negative atoms, then it will calculate the distance between the centre of mass of these two groups.. according to manual. So How can I use g_dist for this kind of calculation. I am little confused. If I take a cut of of 0.4nm (as we mention in g_saltbr), will it be wrong if I have to calculate salt bridges between these two indices - group 1: ASP_GLU__OD1_OD2_OE1_OE2 group 2: ARG_LYS__NZ_NE_NH1_NH2 Thank you Kavya On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 11:58 AM, Kavyashree M wrote: Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Does this really give you any useful information? You'll get an output file with putative contacts derived from an arbitrary cutoff for any possible positive-negative pair defined in the index group. I think the g_dist approach is far more useful and gives you exact insight into specific pairs. It takes a bit more prep work, but looping the calculations is trivial to do to make them efficient. -Justin Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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 -- ==**== 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
Re: [gmx-users] g_density: Segmentation fault
On Tue, Apr 2, 2013 at 12:53 PM, Elisabeth katesed...@gmail.com wrote: Hi Justin, Do I have to read less frames to circumvent the problem? I know g_density has been used for this purpose so there should be a way to resolve this. I am reading 1000 frames... 1000 frames shouldn't be a problem, but it's an easy test to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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 4.6.1 on win7?
On Tue, Apr 2, 2013 at 5:40 AM, Mark Abraham mark.j.abra...@gmail.comwrote: IIRC, the default Cygwin gcc is too old to compile GROMACS, as discussed on this list in the last few months some time. I don't know how easy it is to get a new one via the Cygwin package system. Cygwin has the gcc package which is 3.4.4 and the gcc4 package which offers gcc 4.7.2. Installing the gcc4 package and telling cmake to use gcc-4 as compiler should fix it (not tested). Roland Mark On Mon, Apr 1, 2013 at 5:03 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 1, 2013 at 8:58 AM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx, I tried to install 4.6.1 version through cygwin and got following error by using this command : CMake Error at CMakeLists.txt:811 (message): Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler. When I use SSE4.1 i got this error : CMake Error at CMakeLists.txt:750 (message): Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support. Please need an guidance to install it. Thanks. What compiler (and version) are you using? Apparently whatever is installed does not support the features that Gromacs thinks you should have available. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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: Salt bridge Calculations
On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M hmkv...@gmail.com wrote: Sir, This g_hbond will generate a matrix similar to what g_saltbr would have given in terms of variation of distance between two charge groups. I suppose, in that sense, the output can be useful. I want to find out the variation of all the salt bridges in the protein over the trajectory, if I have to use g_dist with an index of positive atoms and another of negative atoms, then it will calculate the distance between the centre of mass of these two groups.. according to manual. Yes, but that's not what I suggested you do. You would need an index group for each residue individually, not all negative atoms and all positive atoms. That would definitely be useless. If you consider each residue individually, you can get a very detailed look at what's going on. What you're doing now is saying a salt bridge exists if N and O atoms are within 0.4 nm. Is that an accurate descriptor? Upon what precedent have you based that assessment? g_dist will also show you frames where those atoms may not be within 0.4 nm, but what about the case of water-mediated interactions; are those not interesting, as well? What I think you should be doing is approaching the problem from multiple perspectives to get a real look at what's going on. -Justin So How can I use g_dist for this kind of calculation. I am little confused. If I take a cut of of 0.4nm (as we mention in g_saltbr), will it be wrong if I have to calculate salt bridges between these two indices - group 1: ASP_GLU__OD1_OD2_OE1_OE2 group 2: ARG_LYS__NZ_NE_NH1_NH2 Thank you Kavya On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 11:58 AM, Kavyashree M wrote: Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Does this really give you any useful information? You'll get an output file with putative contacts derived from an arbitrary cutoff for any possible positive-negative pair defined in the index group. I think the g_dist approach is far more useful and gives you exact insight into specific pairs. It takes a bit more prep work, but looping the calculations is trivial to do to make them efficient. -Justin Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search http://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_Lists http://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search http://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_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of
Re: [gmx-users] Re: Salt bridge Calculations
Sir, Thank you for the detailed insight. As you mentioned It does not give much information. But the matrix that it would generate would only show whether a specific salt bridge (SB) exited at a given time within the cut-off (0.4). I got your explanation. Yes water mediated SBs are also interesting. If I had a given set of known SB then I would have definitely gone for g_dist. Thank you very much. Kavya On Tue, Apr 2, 2013 at 10:45 PM, Justin Lemkul jalem...@vt.edu wrote: On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M hmkv...@gmail.com wrote: Sir, This g_hbond will generate a matrix similar to what g_saltbr would have given in terms of variation of distance between two charge groups. I suppose, in that sense, the output can be useful. I want to find out the variation of all the salt bridges in the protein over the trajectory, if I have to use g_dist with an index of positive atoms and another of negative atoms, then it will calculate the distance between the centre of mass of these two groups.. according to manual. Yes, but that's not what I suggested you do. You would need an index group for each residue individually, not all negative atoms and all positive atoms. That would definitely be useless. If you consider each residue individually, you can get a very detailed look at what's going on. What you're doing now is saying a salt bridge exists if N and O atoms are within 0.4 nm. Is that an accurate descriptor? Upon what precedent have you based that assessment? g_dist will also show you frames where those atoms may not be within 0.4 nm, but what about the case of water-mediated interactions; are those not interesting, as well? What I think you should be doing is approaching the problem from multiple perspectives to get a real look at what's going on. -Justin So How can I use g_dist for this kind of calculation. I am little confused. If I take a cut of of 0.4nm (as we mention in g_saltbr), will it be wrong if I have to calculate salt bridges between these two indices - group 1: ASP_GLU__OD1_OD2_OE1_OE2 group 2: ARG_LYS__NZ_NE_NH1_NH2 Thank you Kavya On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 11:58 AM, Kavyashree M wrote: Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Does this really give you any useful information? You'll get an output file with putative contacts derived from an arbitrary cutoff for any possible positive-negative pair defined in the index group. I think the g_dist approach is far more useful and gives you exact insight into specific pairs. It takes a bit more prep work, but looping the calculations is trivial to do to make them efficient. -Justin Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search http://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_Lists http://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing list
[gmx-users] Re: g_density: Segmentation fault
Do I have to read less frames to circumvent the problem? I know g_density has been used for this purpose so there should be a way to resolve this. I am reading 1000 frames... 1000 frames shouldn't be a problem, but it's an easy test to do. Sometimes this happens with gromacs analysis utilities if the trajectory is not finished yet (mdrun runs in the same folder and appends the XTC or EDR file) or if certain frame has not been correctly written down. Dr. Vitaly Chaban -- 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: Hamiltonian replica exchange umbrella sampling with gmx 4.6
Hi Micheal, Just to make sure I understand you correctly -- I can have 1 type of restraint, e.g., a harmonic potential between 2 groups defined by (k1, d1) where k1 is force constant and d1 is the equilibrium position. But I can't have 2 or more types of restraints like (k1,d1,k2,d2,...,kn,dn). Is that correct? Also, about to paper you referred to. Is the algorithm described in section IIIB-2 the one that's currently implemented in gromacs? If so, how do you precompute the matrix U for all pairs without knowing x? I guess I just don't have an idea about how the whole procedure is conducted. Thanks, Dejun -- View this message in context: http://gromacs.5086.n6.nabble.com/Hamiltonian-replica-exchange-umbrella-sampling-with-gmx-4-6-tp5006187p5006853.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] the value of pressure is negative
Hi all, I had this problem.When i finished run the equilibration part which is the NPT part, and the time for this equilibration takes is about 500ps. In here,i use the pressure 1 bar and the temperature is 300K, But when i run the command g_energy to check the pressure of the system, the value is negative but the others result is okay. Then i just continue the equilibration.gro to proceed with my md production. And the result for the pressure is 1.5 something and its almost 2 bar for average. Is it normal for that? -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.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] the value of pressure is negative
On 4/2/13 7:56 PM, Nur Syafiqah Abdul Ghani wrote: Hi all, I had this problem.When i finished run the equilibration part which is the NPT part, and the time for this equilibration takes is about 500ps. In here,i use the pressure 1 bar and the temperature is 300K, But when i run the command g_energy to check the pressure of the system, the value is negative but the others result is okay. Then i just continue the equilibration.gro to proceed with my md production. And the result for the pressure is 1.5 something and its almost 2 bar for average. Is it normal for that? http://www.gromacs.org/Documentation/Terminology/Pressure Consider whether 2 ± some hundreds (likely) is significantly different from the target value. -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] g_hbond
Hello, I am calculating the hydrogen bond life time for my system. Do program consider the hydrogen bond criteria for calculation of autocorrelation function? Nilesh -- 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] Radial density calculation
Just calculate the radial distribution function from particle-to-particle. You can then integrate that probability to get a mass density at a given radius, using the average overall system density. 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. -- 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] Radial density calculation
Thank you sir for the nice suggestion On Wed, Apr 3, 2013 at 9:58 AM, Dallas Warren dallas.war...@monash.eduwrote: Just calculate the radial distribution function from particle-to-particle. You can then integrate that probability to get a mass density at a given radius, using the average overall system density. 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. -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
