[gmx-users] Re: Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)
I have gone through the pull parameters in version 4.0 and 4.5 a bit more after our previous discussion and I have found the following related to the value of pull_init1. pull_geometry = distance or direction generate the same distance at start with grompp no matter what value is set to pull_init1, and it is the same in version 4.0 as in 4.5. However, for pull_geometry = cylinder in version 4.5 I find that the measured distance at start varies with the value on pull_init1. For a molecule at distance -0.026 nm from the reference group (value from version 4.0) I obtain the following with grompp in version 4.5: pull_init1 = 0 gives start distance -0.026 pull_init1 = 1 gives start distance -0.026 pull_init1 = 2 gives start distance 0.605 pull_init1 = 3 gives start distance 2.596 pull_init1 = 4 gives the error that the distance of the pull group is larger than 0.49 times the box size. In version 4.0, all values of pull_init1 generate the distance at start = -0.026. I will set pull_init1 to -0.026 or use pull_start = yes in this case and it would give the result that I want. From these findings I assumed that the value of pull_init1 was somehow added to the measured distance in version 4.5. However, for another system in which the distance between the groups is -2.996 nm, the following is obtained: pull_init1 = 0 gives start distance -0.465 pull_init1 = 1 gives start distance 1.014 pull_init1 = 2 gives the error that the distance of the pull group is larger than 0.49 times the box size. pull_init1 = 3 gives the error that the distance of the pull group is larger than 0.49 times the box size. pull_init1 = 4 gives the error that the distance of the pull group is larger than 0.49 times the box size. Here, pull_init1 = 3 can thus not be used; opposite to the previous case in which a value of pull_init1 close to the measured distance seemed to work. If I instead use pull_geometry = distance or direction all values of pull_init1 generate the error that the distance of the pull group is larger than 0.49 times the box size. In version 4.0, the value of pull_init1 does, again, not affect the distance at start. I interpret pull_init1 as the reference distance at start (i.e. the initial distance that I want to constrain as I am not pulling the molecule) and I thought that this should not affect the measured distance at start that grompp displays, at least that is what can be concluded from version 4.0. Could someone please help me to figure this out? Thanks. Emma On 2012-10-08 09:05, Emma Eriksson wrote: Thank you David for your response. Please see my reply below. On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DMPC pull_group1 = 2 pull_vec1 = 0 0 1 pull_init1 = x I have previously been using the same methodology in 4.0.5 without problems. When i run grompp in 4.5.5 I get the following error: Fatal error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310) The source of the first value, which should be the distance of pull group 1 is for me unknown. A value of ~4 is generated for all systems no matter what z distance is actually betwen the two groups (0-4 nm), so the value has no connection to the z distance between the groups. The second value is 0.5 times the x box length. I have read through pull.c, but I cannot find an explanation to why the x direction seems to be considered and not the z direction. When I run grompp with pull_geometry = distance or direction together with pull_dim = N N Y there is no problem. As I am not sure of the source of this error when running with cylinder I do not know if it is only related to the check or if the following simulation would be affected if I uncomment the check. Any suggestions to why this is happening and what I can do about it? Check the other pull_XXX values in mdout.mdp You have not specified all of them above, e.g. pull_direction? The pull parameter section in mdout.mdp are the following: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint ; Pull geometry: distance, direction, cylinder or position pull_geometry= cylinder ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1.0 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol
Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX
On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX
Hi David: I have tested the script. The input are 1 charmm topology file, 2 corresponding charmm parameter file and 3 foldername. But there are a lots of top_all***.rtf files and par_all***.prm files in toppar_c36_aug12/toppar folder, I don't know which pair is the correct pair. Could you give me a clue? The new parameter for cholesterol is stored in chol_new.str. If it is OK that I just put chol_new.str into the toppar_c36_aug12/toppar/ folder and transfer it directly. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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] Getting the constraint force from the LINCS algorith
Dear Gromacs user, This question is directed foremost on Berk Hess, but it may be interesting also for other users. Berk Hess evaluated the force between two ions separated by the LINCS algorithm (Berk Hess et al Osmotic coefficients of atomistic NaCl force fields). My question is, how did he do this? g_energy is not able to provide me with this output. Searching the mailing list, the web and the manual gave me no result. I know there are other methods to constrain the distance between two ions (shake, bonds etc.) but as the LINCS algorithm is effective in keeping the distance on the ions, I would like to use that. Many thanks in advance, Best Tom Kirchner -- 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] Simulation of charged systems
Dear Colleagues, I am currently carrying out MD simulations on models of archaeal membranes. These membranes, contrary to those of bacteria or eukariota, are made of unconventional lipids. In my case they contain a neutral carbohydrate headgroup and the second one is a negatively charged phospho-myoinositol, contrary to neutral (zwitterionic) phosphocholine found in conventional lipids. In order to have a neutral system to carry out the simulation on: 1. I could add 36 positive counterions (eg, Na+) to my membrane model, which would correspond to approx. 900 mM of these ions for the amount of water molecules I am using. This concentration is of course not only much higher than a physiological one, although it is, strictly speaking, not a salt, i.e. NaCl, concentration. The issue is that I would like to study the effect of salt (alkali cations) on the membrane properties and therefore would need a suitable, possible ion/salt-free system as reference state. 2. I could protonate the phosphate and have -O-P(OOH)-O- instead of -O-P(O2-)-O-. This would provide a neutral, salt-free reference state, but the issue is that this phosphate group would be probably de-protonated in the cellular compartment it is localized, which has a pH of approx 6. Another option would be to run the simulations on the charged system, without counterions, but I am not quite sure if there are technical problems with that. I am using the following settings for the treatment of long-range electrostatics: ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT I wonder if someone could kindly advise me in this issue. Any suggestion or comment will be highly appreciated. Best regards, Felipe +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Linnaeus University | | SE-391 82 Kalmar | | Sweden - Sverige | +---+ -- 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] Defining strongly interdependent dihedral force constants
I'm trying to model a species for which the force field I'm using (OPLS-AA) doesn't contain all the force constants needed for some of the groups present. I've successfully defined several angle and dihedral force constants using quantum mechanical simulations to generate potential energy curves and I'm happy that the method works, however there are a few that I'm struggling with. The specific dihedrals are adjacent ones between aromatic rings with a bridging atom between, e.g CA-CA-X-CA' and CA-X-CA'-CA', where the CA atoms are part of a phenyl ring and CA' atoms are in a napthyl group (Napth-X-Ph). It seems that there is a large amount of inter-dependence between the two dihedrals to the degree that the energy difference I'm trying to fit for one varies significantly with the value of the other angle. Fixing one dihedral at its most favourable angle and fitting the other (and vice-versa) results in a potential energy surface that is quite different to that obtained by quantum mechanics. Has anyone else managed to fit a similar system with strongly coupled dihedrals? Any suggestions or advice would be much appreciated! -- View this message in context: http://gromacs.5086.n6.nabble.com/Defining-strongly-interdependent-dihedral-force-constants-tp5002539.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] fraction of native contacts calculation
31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Cholesterol parameters (Charrm36) in GMX
On 2012-11-01 09:47, Yorquant Wang wrote: Hi David: I have tested the script. The input are 1 charmm topology file, 2 corresponding charmm parameter file and 3 foldername. But there are a lots of top_all***.rtf files and par_all***.prm files in toppar_c36_aug12/toppar folder, I don't know which pair is the correct pair. Could you give me a clue? The new parameter for cholesterol is stored in chol_new.str. If it is OK that I just put chol_new.str into the toppar_c36_aug12/toppar/ folder and transfer it directly. Don't know. I think you need everything gromacs related that comes out. Do it in an empty directory. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tc-grps in Temperature coupling
On 11/1/12 9:19 AM, Ali Alizadeh wrote: Dear All users What difference is between two codes? Read this: http://www.gromacs.org/Documentation/Terminology/Thermostats. I don't know what LI and LG are (lithium and something else?) but likely the latter approach is not correct. -Justin ; Temperature coupling is on tcoupl= berendsen tc-grps= System --- whole system tau_t= 0.1 ref_t= 240 ; Pressure coupling is on pcoupl= berendsen pcoupltype= isotropic tau_p= 2.0 ref_p= 300.0 compressibility = 4.5e-5 - ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps= SOL LILG --- selecting groups tau_t = 0.1 0.10.1; ps ref_t = 240 240240; K Pcoupl = berendsen Pcoupltype = isotropic tau_p = 2 compressibility = 4e-5 ref_p = 300 -- 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] regarding converge of system
Hi, I have two questions: 1-We can say The RMSD is commonly used as an indicator of convergence of the structure towards an equilibrium state (Tsjerk W.). RMSD is not sufficient to determine whether or not converge of structure/system. Why? 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- 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] regarding converge of system
RMSD of what? Probably you mean RMSD from the starting (or crystal) structure. First, consider that your profile of RMSD vs. crystal structure levels off at 0.4 nm with increasing simulation time. Consider how many possible conformations are 0.4 nm RMSD away from the crystal structure. A stable RMSD does not necessarily indicate that you have obtained Boltzmann sampling of a particular conformational basin. Very generally, it is the degeneracy of RMSD with respect to conformational space that makes RMSD an insufficient indicator of convergence. There are other ways to look at this though. For instance, there might be an important degree of freedom that is important for your system but does not greatly affect the global conformation (and thus the RMSD). This might be a dihedral angle, formation of a hydrogen bond, tilt/rotation of a protein/peptide in a lipid bilayer, solvation patterns, ligand binding, system volume, etc. Also, and I presume that this is not what Tsjerk meant (but you should check whatever reference you are referring to) it is always possible that you remain stuck within a conformational basin that is locally favourable but globally unfavourable. For other measures of convergence, first think about what you are trying to study for your system and use that to guide your selection of properties for which you can evaluate convergence. This should include both global and local structural measures. There are loads of papers available that discuss this. See papers by Grossfield, Zuckerman, and others. A colleague of mine has also shown that some properties converge faster than others (meaning that some properties, like the RMSD, converge before the partition function has converged: http://pubs.acs.org/doi/abs/10.1021/ct900302n ). Chris. -- original message -- I have two questions: 1-We can say The RMSD is commonly used as an indicator of convergence of the structure towards an equilibrium state (Tsjerk W.). RMSD is not sufficient to determine whether or not converge of structure/system. Why? 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- 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] Regarding g_tune_pme optimization
Dear all Gromacs users, I have *two *questions: 1) I have been doing my simulation on a computer having 24 processors. I issued *g_tune_pme -s *.tpr -launch *command to directly launch my *mdrun *with the optimized settings. At the end of optimization, g_tune_pme has given -npme as *'0'*. My doubt is, how could it be possible to get best performance without dedicated PME nodes? 2) What could be the optimum value for *-rcom *to get the best performance on a super cluster (*i.e., 256 nodes*)? Thanks in advance 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
[gmx-users] carbohydrate forcefield in gromacs
Hi, Is carbohydrate forcefield in Charmm or Amber included in gromacs4.5.5 topology folders ? Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] are wall atoms virtual ?
Dear all, My system consists of Two walls of carbon atoms but I am not able to view the carbon atom walls in VMD. Also my topology file have no information about wall atoms. So is it possible to see them somehow or my system has no walls indeed ? -- View this message in context: http://gromacs.5086.n6.nabble.com/are-wall-atoms-virtual-tp5002549.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] Regarding g_tune_pme optimization
Hi, On Nov 1, 2012, at 4:13 PM, Venkat Reddy venkat...@gmail.com wrote: Dear all Gromacs users, I have *two *questions: 1) I have been doing my simulation on a computer having 24 processors. I issued *g_tune_pme -s *.tpr -launch *command to directly launch my *mdrun *with the optimized settings. At the end of optimization, g_tune_pme has given -npme as *'0'*. My doubt is, how could it be possible to get best performance without dedicated PME nodes? This is normal, it just means that 24 PME nodes are optimal and thus no *separate* PME nodes are needed. Carsten 2) What could be the optimum value for *-rcom *to get the best performance on a super cluster (*i.e., 256 nodes*)? Thanks in advance 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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 APL And Shrunken System Size
I gave My cmd Prompt output for satisfactorily shrunken system as follows Reading. Scaling lipids There are 127 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 63 lipids in the lower leaflet Centering protein Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 98 119 Protein Y-min/max: 99 117 X-range: 21 A Y-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 3.75 nm^2 Area per lipid: 6.60886502362205 nm^2 Area per protein, upper half: 2.75 nm^2 Area per lipid, upper leaflet : 6.572858265625 nm^2 Area per protein, lower half: 3 nm^2 Area per lipid, lower leaflet : 6.67322109523809 nm^2 Writing Area per lipid... In the final Energy minimization (.gro file) of the satisfactorily shrunken system The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 Then As you Told Me the There is Something wrong Because Such Large x-y Area is not Possible with Quoted APL ( 6.60886502362205 nm^2) May I Increase the Initial box size ? Why this Happens and Where I have Committed the Mistake ? My system is Cyclic Peptide I am grateful if you Give suggestion and Commments Thanks In Advance Done! -- 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 APL And Shrunken System Size
On 11/1/12 12:48 PM, vidhya sankar wrote: I gave My cmd Prompt output for satisfactorily shrunken system as follows What was your command that produced this output? Reading. Scaling lipids There are 127 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 63 lipids in the lower leaflet Centering protein Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 98119 Protein Y-min/max: 99117 X-range: 21 AY-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 3.75 nm^2 Area per lipid: 6.60886502362205 nm^2 Area per protein, upper half: 2.75 nm^2 Area per lipid, upper leaflet : 6.572858265625 nm^2 Area per protein, lower half: 3 nm^2 Area per lipid, lower leaflet : 6.67322109523809 nm^2 Writing Area per lipid... In the final Energy minimization (.gro file) of the satisfactorily shrunken system The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 Please use real file names and tell me where this comes from. Then As you Told Me the There is Something wrong Because Such Large x-y Area is not Possible with Quoted APL ( 6.60886502362205 nm^2) Yes, it is absolutely impossible to have that APL in a system that has an x-y area of over 42000 A^2. I suspect you're confusing your files. May I Increase the Initial box size ? I have already suggested that you make no manual modifications to box vectors. Why this Happens and Where I have Committed the Mistake ? My system is Cyclic Peptide I am grateful if you Give suggestion and Commments Please answer all questions posed above directly. I suspect you are mixing up files but I can't possibly guess what is going on. Your assertions do not add up and I can't suggest a resolution without complete information. -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] why it is so slow
hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s remd_.tpr -multi 16 -replex 300 I found that it will require 1 months to be finished which is a really long time. I am just wondering is there anything I did wrong for the .mdp so that it is so slow? here is my .mdp file. thank you very much title = Protein-ligand complex NPT equilibration ; Run parameters integrator = sd ; nsteps = 2000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs nstxout = 0 ; save coordinates every 0.2 ps nstvout = 0 ; save velocities every 0.2 ps nstfout = 0 nstxtcout = 500 nstenergy = 100 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps energygrps = Protein_LIG ; Bond parameters continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0 ; short-range electrostatic cutoff (in nm) rvdw = 0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cutoff ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.15 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_LIG ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 310 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; pressure coupling is on for NPT ; Periodic boundary conditions ; Pressure coupling pcoupl = no; pressure coupling is on for NPT ; Periodic boundary conditions tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar pbc=no ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme pcoupltype = isotropic ; uniform scaling of box vectors ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 310 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ld_seed=-1 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = GBSA comm_mode = ANGULAR ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = OBC ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 0 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.25936 -- 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] why it is so slow
On 11/1/12 12:55 PM, Albert wrote: hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. Based on your .mdp file, you're not doing NPT (pcoupl = no). mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s remd_.tpr -multi 16 -replex 300 I found that it will require 1 months to be finished which is a really long time. I am just wondering is there anything I did wrong for the .mdp so that it is so slow? here is my .mdp file. One month is not very long, especially if you are running on CPU and not GPU. How many atoms are in your system? How did you decide that 24 CPU per replica was appropriate? How did you decide on your exchange frequency? Exchanging every 0.6 ps sounds awfully frequent, but I'm no REMD expert so I'll leave that for others to comment on. -Justin thank you very much title = Protein-ligand complex NPT equilibration ; Run parameters integrator = sd ; nsteps = 2000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs nstxout = 0 ; save coordinates every 0.2 ps nstvout = 0 ; save velocities every 0.2 ps nstfout = 0 nstxtcout = 500 nstenergy = 100 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps energygrps = Protein_LIG ; Bond parameters continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0 ; short-range electrostatic cutoff (in nm) rvdw = 0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cutoff ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.15 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_LIG ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 310 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; pressure coupling is on for NPT ; Periodic boundary conditions ; Pressure coupling pcoupl = no; pressure coupling is on for NPT ; Periodic boundary conditions tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar pbc=no ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme pcoupltype = isotropic ; uniform scaling of box vectors ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 310 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ld_seed=-1 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = GBSA comm_mode = ANGULAR ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = OBC ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 0 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.25936 -- 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] fraction of native contacts calculation
Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- --- *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
Re: [gmx-users] fraction of native contacts calculation
On 11/1/12 1:23 PM, bipin singh wrote: Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. If someone writes the code, certainly. Gromacs is a user-driven community, after all :) If there is a feature you want, file a feature request on redmine.gromacs.org, otherwise no one is likely to pay much attention to it, as other, much larger changes are ongoing. -Justin On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Re, g_rdf
On 11/1/12 12:25 PM, Ali Alizadeh wrote: Dear Justin These attachments are my rdf,g(r) profiles, http://tb18.trainbit.com/d/8692999884.jpg http://tb18.trainbit.com/d/6692999884.jpg http://tb18.trainbit.com/d/9692999884.jpg You've got an inhomogeneous system; you can't expect it to behave like a homogeneous system. For a system of pure water, convergence to 1 is expected. For a multi-layer system like this one, I don't know what the expected outcome is for the RDF. -Justin Dear All users I have a system that contains water , methane and propane in 240 k and 300 bar, My simulation box is rectangular . Water film is in middle of my box. Methane and propane is around it. My simulation box is symmetric, 1- I used g_rdf program for . My result is exotic. My g(r) in profile do not reach to ! Why 2- I test my number density profiles(from g_density) but they do not correct result because when i calculate number of my molecules by multiplying volume to average number density, i can not take the same number of my particle, Where do i mistake? -- 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] fraction of native contacts calculation
Thanks for the information. On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/1/12 1:23 PM, bipin singh wrote: Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. If someone writes the code, certainly. Gromacs is a user-driven community, after all :) If there is a feature you want, file a feature request on redmine.gromacs.org, otherwise no one is likely to pay much attention to it, as other, much larger changes are ongoing. -Justin On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -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 --**- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/**elflab/index.htmlhttp://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- --- *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
Re: [gmx-users] fraction of native contacts calculation
Bipin, There might be a workaround. You might want to check out Plumed plugin in latest versions of VMD for calculating fractions of native contact. You can load the gromacs trajectory along with the native .gro file in VMD and use Plumed plugin inbuilt in VMD . You need to install plumed most probably early. From: bipin singh bipinel...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 1, 2012 1:23 PM Subject: Re: [gmx-users] fraction of native contacts calculation Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -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 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- --- *Regards,* Bipin Singh -- 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
Re: [gmx-users] fraction of native contacts calculation
Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. In the meantime you might be able to use MDAnalysis http://mdanalysis.googlecode.com/ and the native contact analysis in MDAnalysis.analysis.contacts, see http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html (If you have questions about MDAnalysis then please ask them on that project's discussion group http://groups.google.com/group/mdnalysis-discussion — people there are more than happy to help.) Best wishes, Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://becksteinlab.physics.asu.edu/ Arizona State University Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: http://physics.asu.edu/home/people/faculty/oliver-beckstein Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343 -- 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] fraction of native contacts calculation
Thanks a lot Oliver for the useful information. On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein obeck...@asu.edu wrote: Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. In the meantime you might be able to use MDAnalysis http://mdanalysis.googlecode.com/ and the native contact analysis in MDAnalysis.analysis.contacts, see http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html (If you have questions about MDAnalysis then please ask them on that project's discussion group http://groups.google.com/group/mdnalysis-discussion — people there are more than happy to help.) Best wishes, Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://becksteinlab.physics.asu.edu/ Arizona State University Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: http://physics.asu.edu/home/people/faculty/oliver-beckstein Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343 -- 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 -- --- *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] Hessian Unit
hi Gmxers, is the Hessian matrix unit in gmx is ps^(-2), or J *mol^(-1) nm^(-2)? thanks, Yao -- -- 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] fraction of native contacts calculation
Thanks a lot Sanku for your help. On Thu, Nov 1, 2012 at 11:38 PM, Sanku M msank...@yahoo.com wrote: Bipin, There might be a workaround. You might want to check out Plumed plugin in latest versions of VMD for calculating fractions of native contact. You can load the gromacs trajectory along with the native .gro file in VMD and use Plumed plugin inbuilt in VMD . You need to install plumed most probably early. From: bipin singh bipinel...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 1, 2012 1:23 PM Subject: Re: [gmx-users] fraction of native contacts calculation Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- --- *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 -- --- *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
Re: [gmx-users] regarding converge of system
Hey :) If I say something is commonly used, I don't mean that the usage is correct :p Chris' answer is quite good though, and I can't add much more, except maybe that the RMSD, being a distance, isn't a good indicator of convergence, when it reaches the point of saying 'far away'. There's just too much far away; the conformational space associated with an RMSD of 0.7 or more is huge! So if a structure stays at that distance, it may still be flying around like there's no tomorrow. The convergence of the RMSD against the average structure will be better, and so is the drift in the average structure itself. Note though, that these may still show apparent (or false) convergence if they stay in a particular region of conformational space. Cheers, Tsjerk On Thu, Nov 1, 2012 at 3:13 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: RMSD of what? Probably you mean RMSD from the starting (or crystal) structure. First, consider that your profile of RMSD vs. crystal structure levels off at 0.4 nm with increasing simulation time. Consider how many possible conformations are 0.4 nm RMSD away from the crystal structure. A stable RMSD does not necessarily indicate that you have obtained Boltzmann sampling of a particular conformational basin. Very generally, it is the degeneracy of RMSD with respect to conformational space that makes RMSD an insufficient indicator of convergence. There are other ways to look at this though. For instance, there might be an important degree of freedom that is important for your system but does not greatly affect the global conformation (and thus the RMSD). This might be a dihedral angle, formation of a hydrogen bond, tilt/rotation of a protein/peptide in a lipid bilayer, solvation patterns, ligand binding, system volume, etc. Also, and I presume that this is not what Tsjerk meant (but you should check whatever reference you are referring to) it is always possible that you remain stuck within a conformational basin that is locally favourable but globally unfavourable. For other measures of convergence, first think about what you are trying to study for your system and use that to guide your selection of properties for which you can evaluate convergence. This should include both global and local structural measures. There are loads of papers available that discuss this. See papers by Grossfield, Zuckerman, and others. A colleague of mine has also shown that some properties converge faster than others (meaning that some properties, like the RMSD, converge before the partition function has converged: http://pubs.acs.org/doi/abs/10.1021/ct900302n ). Chris. -- original message -- I have two questions: 1-We can say The RMSD is commonly used as an indicator of convergence of the structure towards an equilibrium state (Tsjerk W.). RMSD is not sufficient to determine whether or not converge of structure/system. Why? 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] regarding converge of system
Dear Christopher, Firstly thanks for your reply. RMSD is a measure related with whether or not converge of particles in the structures versus the starting structure. In other word, it is the difference (average distance) between the positions of particles in two structures. Conformational changes is not only on the change of the position of atoms/particles in the structure but also depend on other parameters (dihedral angle, formation of a hydrogen bond, tilt/rotation of a protein/peptide in a lipid bilayer, solvation patterns, ligand binding, system volume, etc). Am I wrong? RMSD matrix is also used to control the convergence of the structure. What is the main difference between RMSD and RMSD matrix? Thanks in advance 2012/11/1 Christopher Neale chris.ne...@mail.utoronto.ca RMSD of what? Probably you mean RMSD from the starting (or crystal) structure. First, consider that your profile of RMSD vs. crystal structure levels off at 0.4 nm with increasing simulation time. Consider how many possible conformations are 0.4 nm RMSD away from the crystal structure. A stable RMSD does not necessarily indicate that you have obtained Boltzmann sampling of a particular conformational basin. Very generally, it is the degeneracy of RMSD with respect to conformational space that makes RMSD an insufficient indicator of convergence. There are other ways to look at this though. For instance, there might be an important degree of freedom that is important for your system but does not greatly affect the global conformation (and thus the RMSD). This might be a dihedral angle, formation of a hydrogen bond, tilt/rotation of a protein/peptide in a lipid bilayer, solvation patterns, ligand binding, system volume, etc. Also, and I presume that this is not what Tsjerk meant (but you should check whatever reference you are referring to) it is always possible that you remain stuck within a conformational basin that is locally favourable but globally unfavourable. For other measures of convergence, first think about what you are trying to study for your system and use that to guide your selection of properties for which you can evaluate convergence. This should include both global and local structural measures. There are loads of papers available that discuss this. See papers by Grossfield, Zuckerman, and others. A colleague of mine has also shown that some properties converge faster than others (meaning that some properties, like the RMSD, converge before the partition function has converged: http://pubs.acs.org/doi/abs/10.1021/ct900302n ). Chris. -- original message -- I have two questions: 1-We can say The RMSD is commonly used as an indicator of convergence of the structure towards an equilibrium state (Tsjerk W.). RMSD is not sufficient to determine whether or not converge of structure/system. Why? 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- 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 -- Ahmet Yıldırım -- 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] T - Annealing at NP - cell expands
On 11/1/12 4:36 PM, Steven Neumann wrote: Dear Gmx Users, I have system with protein in water. I equlibrated it in at 300 K and 1 bar for 5 ns with position restrained of protein heavy atoms. I run script at NP and increasing temperature from 300K to 600 K with changing temperature of 1 Kelvin every 1000 steps. Then temperaure is set to be 600 K for another 4 ns to cool it down after to 300K within 2 ns. System fails when the temperature reached 600K - my box is being expanded during the temperature increase TWICE! This is why it fails and my job terminates. Would you suggest something? A complete .mdp file would be useful here (just in case), although the observed behavior doesn't sound too unusual to me. Under constant pressure, when you heat a liquid, what happens? 600K is well above the boiling point of water, so it sounds to me like your unit cell is simply responding to what you're doing. Perhaps you should be using NVT, but I don't know what your purpose for this procedure is. -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] Freeze group atoms changing position
I've created a position restraint file for the specific waters that I need to immobilize, but I'm having a hard time getting grompp to apply it successfully. No matter where I put #include posre.itp in my topology file grompp returns fatal errors about the atomic indices being out of bounds. Is it actually possible to only apply position restraints to some molecules within a species and leave the rest alone? On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/12 3:55 PM, Alex Marshall wrote: Chris, is that for freeze groups or position restraints? I will assume Chris was referring to the restraint method - you need an index file for creating the position restraint .itp file using genrestr. It will save you a ton of time over doing it manually. -Justin On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall amarsh59 at uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcostescu at gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amarsh59 at uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- gmx-users mailing listgmx-users at 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-request at gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- 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
Re: [gmx-users] T - Annealing at NP - cell expands
On Thu, Nov 1, 2012 at 8:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/1/12 4:36 PM, Steven Neumann wrote: Dear Gmx Users, I have system with protein in water. I equlibrated it in at 300 K and 1 bar for 5 ns with position restrained of protein heavy atoms. I run script at NP and increasing temperature from 300K to 600 K with changing temperature of 1 Kelvin every 1000 steps. Then temperaure is set to be 600 K for another 4 ns to cool it down after to 300K within 2 ns. System fails when the temperature reached 600K - my box is being expanded during the temperature increase TWICE! This is why it fails and my job terminates. Would you suggest something? A complete .mdp file would be useful here (just in case), although the observed behavior doesn't sound too unusual to me. Under constant pressure, when you heat a liquid, what happens? 600K is well above the boiling point of water, so it sounds to me like your unit cell is simply responding to what you're doing. Perhaps you should be using NVT, but I don't know what your purpose for this procedure is. -Justin Thanks for your reply. I am trying to get parametrs for coarse grained model so I want to repeat this procedure until covergence. Do you think NVT could be used for this purpose? Steven -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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] I have a problem with my biphasic system
On 11/1/12 5:49 PM, Ali Alizadeh wrote: Dear All usres I have a system that contains water , methane and propane in 240 k and 300 bar, My simulation box is rectangular . Water film is in middle of my box. Methane and propane is around it. I have a problem, my methane and propane molecules do not diffuse in water film(even my methane molecules), I do simulation, 30 nano second methane molecules = 834 propane molecules = 92 water molecules = 1656 These links is related to md.mdp and .mdp for energy minimization http://trainbit.com/files/1132999884/md.mdp http://trainbit.com/files/2132999884/minim.mdp The permissions on your files are set such that no one else can view them. Why would you expect your alkanes to dissolve in water? The solubility of methane is very small (roughly 0.02 g/kg of water at 25 C, or about 0.0014 M). Given this information, in your very small system, basically no methane molecules would ever partition into the water layer. I didn't do the back-of-the-envelope calculations for propane, but you get the idea. -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] About BoxVector and APL
As uou Told me in the Previous Mail I have Given My sereis of Commands With Real file Names ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3 -box 6 6 6 ./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top -o emdppc.tpr -maxwarn 1 ./trjconv_d -s emdppc.tpr -f dppc128n.gro -o dppc128_whole.gro -pbc mol -ur compact ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c cat 2KDQ_newbox.gro dppc128_whole.gro system.gro ./genrestr_d -f 2KDQ_newbox.gro -o strong_posre.itp -fc 10 10 10 perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr ./mdrun_d -v -deffnm 2KDQDPPCem perl inflategro.pl 2KDQDPPCem.gro 0.95 DPPC 0 system_inflated1.gro 5 area1.dat ./grompp_d -f emdppc.mdp -c system_inflated1.gro -p 2KDQ.top -o 2KDQDPPCem1.tpr ./mdrun_d -v -deffnm 2KDQDPPCem1 perl inflategro.pl 2KDQDPPCem1.gro 0.95 DPPC 0 system_inflated2.gro 5 area2.dat ./grompp_d -f emdppc.mdp -c system_inflated2.gro -p 2KDQ.top -o 2KDQDPPCem2.tpr ./mdrun_d -v -deffnm 2KDQDPPCem2 perl inflategro.pl 2KDQDPPCem2.gro 0.95 DPPC 0 system_inflated3.gro 5 area3.dat output for My satisfactorily shrunken system as follows Reading. Scaling lipids There are 127 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 63 lipids in the lower leaflet Centering protein Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 98 119 Protein Y-min/max: 99 117 X-range: 21 A Y-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 3.75 nm^2 Area per lipid: 6.60886502362205 nm^2 Area per protein, upper half: 2.75 nm^2 Area per lipid, upper leaflet : 6.572858265625 nm^2 Area per protein, lower half: 3 nm^2 Area per lipid, lower leaflet : 6.67322109523809 nm^2 Writing Area per lipid. ./grompp_d -f emdppc.mdp -c system_inflated3.gro -p 2KDQ.top -o 2KDQDPPCem3.tpr ./mdrun_d -v -deffnm 2KDQDPPCem3 In the final Energy minimization (2KDQDPPCem3.gro file) of the satisfactorily shrunken system The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 As you're suspecting I may be confusing your files. In the beginning I am giving Series of Commands with Real files Name Could you Please Suggests Where i Have Confused in File Names ? Kindly Give me your Valuable Suggestion Thanks In Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about tc_grps in mdp file...
Dear all, I am running a system with sol 40646 atom and ion, NA 629 CL 634. At the time of nvt and npt should i have to make different *tc_grps* for ion and sol or should be make one group Nonprotein ( these include sol + ion)..these is default. With Best wishes and 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
