[gmx-users] Re: Anomaly in Temperature Behavior
S. Alireza B wrote It appears that my solid phase completely melts after 700 ps. Please see the video below. http://www.youtube.com/watch?v=6iidpiivVRIfeature=youtu.be Can I conclude that my solid phase is not really far from the equilibrium as it does not suddenly melt/collapse? Yes, i would conclude the same looking at this video. 1) Do you still have the problem that the temperature keeps increasing (but not decreasing) over the 700 ps simulation ? If this is true, then it looks strange to me. Then, i would think that the problem could with with the poor energy conservation in the system. Such, gmx developers suggest to use PME-switch instead of PME. PME-Switch A combination of PME and a switch function for the direct-space part (see above). rcoulomb is allowed to be smaller than rlist. This is mainly useful constant energy simulations. Here, one should note that PME in gromacs is not exactly the same as in other MD codes. In gromacs PME there is no cut-off for the real space Ewald sum. But one could force it to do the cut-off with the switching function on a tiny distance interval using PME-Switch. Whether it improves the energy conservation, i do not know. In this discussion http://redmine.gromacs.org/issues/196; it is stated that Gromacs PME ... can conserve energy better in single precision than either Desmond, NAMD, Amber or Charmm do in double. Thus, to me it is not clear why actually in the online manual it is suggested to use PME-Switch for energy conservation. Anyway, i never did NVE simulations, so can not be much of help here. 2) Comment 1: are you aware of ewald_geometry = 3dc ? If you want to simulate 2d periodic system (slab) in vacuum then this would be the correct setup. If you want a 3d periodic system of infinite number of slabs, which interact with each other, then the current setup is correct. 3) Comment 2: you start your NVE simulation with zero velocities on the molecules of solid phase (and, thus, zero temperature of the solid phase). In this setup to melt the solid, one has to 1) heat the solid phase up to its melting temperature and 2) melt it. Is it what you want to do ? Andrey -- View this message in context: http://gromacs.5086.n6.nabble.com/Anomaly-in-Temperature-Behavior-tp5004808p5005142.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] Dynamics of the salt-bridges
Hi, If you don't care about the exact distances, but rather the time the groups spend within a certain distance, g_hbond -contact can be useful. Best, Erik On Feb 3, 2013, at 6:36 PM, James Starlight wrote: Justin, 1 )for example I want to select in index file only all asp, glu and his residues ( I could find selection by residue type only). 2) Than I'd like that gromacs compute dynamics of the distance between that charge groups (providing only truncated .tpr file as the input) but only. Could other than g_saltbr gromacs tools be used for that (E,g g_dist ) ? James 2013/2/3 Justin Lemkul jalem...@vt.edu: On 2/3/13 1:01 AM, James Starlight wrote: Justin, thanks again for suggestions. I'm not quite sure how I can use tpbconv -zeroq. For example I want to reduce charges of all amino acids except Asp Glu and His ( to monitor s.b dynamics between that groups only). As I understood -zeroq working with the groups defined in the index file so I should just select all residues that I need in that file, shouldnt it ? Also doest it possible to select pairs of residues Yes. placed in the sequence on the distant sites ? (e.g by selecting only pairs within some range of n1 and n2+k where kn1+10) I don't understand what you mean. tpbconv will only take one index group for zeroing charges, so I don't understand how such a relative scheme would work for all cases. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] steepest descents followed by conjugated gradient
Hi Justin i see lots of papers perform steepest descent followed by conjugated gradients. My question do i use the .gro output file as input to perform conjugated gradient minimization as shown in the commands below? or do i repeat pdb2gmx, editconf and genbox on the trajectory file (protA_em.trr) which i must convert to a .pdb file? nohup mdrun -s protA_em.tpr -o protA_em.trr -c *protA_b4pr.gro* -g em.log -e em.edr Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 1000 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 754 steps Potential Energy = -6.8864319e+05 Maximum force = 9.1053461e+02 on atom 499 Norm of force = 2.2879843e+01 Now i run conjugated gradient (500 steps) grompp -f em2.mdp -c *protA_b4pr.gro* -p Rv1712.top -o protA_1em.tpr nohup mdrun -s protA_1em.tpr -o protA_em1.trr -c protA_b4pr_1.gro -g em.log -e em.edr when i run these i get an error message segmentation fault? which i know is usually a memory problem. Thanks Ruben -- 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] How to analysis 10 ns from 20 ns simulation
HI, It should read trjconv. And all analysis tools have the -b and -e flags for excluding the start or the end of a trajectory. Erik On Feb 4, 2013, at 7:00 AM, Emanuel Birru wrote: Use trajconv http://manual.gromacs.org/online/trjconv.html -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org ] On Behalf Of Naga Sundar Sent: Monday, 4 February 2013 4:45 PM To: Discussion list for GROMACS users Subject: [gmx-users] How to analysis 10 ns from 20 ns simulation Dear users I performed 20 ns simulation for protein complex. After 10 ns only my system obtained equilibration state . I would like to analyze last 10 ns from the trajectory file.I got problem to generate last 10 ns xtc file from the 20 ns trr file. so, plz help me to sort out this problem -- Regards N.NagaSundaram -- 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] npt error
hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the error message as inner product between old and new vector is 0.0 and water molecules starting at atom 3892 cannot be settled ,check for bad contacts, change the time scale can anyone suggest solution for this . i could not find what the reason will be .i will be waiting for the answer thankyou -- with regards, Rajalakshmi Molecular Modelling simulations lab IIT Madras chennai-36 -- Open WebMail Project (http://openwebmail.org) -- 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] confusion about pdb file and coordinate.xvg file
Hi all, I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version. I have generated the trajectory file using trjconv utility in gromacs. Using the trr file used to generate the .pdb file, I have generated the co-ordinates of H atoms of water using g_traj utility. I thought I will get the same value of co-ordinates of H atoms in both the files in a particular time step. But it was not so. I am attaching here a part of both the files containing the co-ordinates of H atoms in the first time step. Please note that I have modified and removed the co-ordinates of oxygen atoms from the pdb file. My doubts are: 1. Am I wrong in thinking that in both the files, co-ordinates of same atoms in a particular time step should be same? 2. If I am wrong, then what is correct ? 3. If I am correct then what may be the possible cause of having different coordinates in both the files? Thanks, Best Regards, Biki traj.pdb http://gromacs.5086.n6.nabble.com/file/n5005150/traj.pdb Hcoord.xvg http://gromacs.5086.n6.nabble.com/file/n5005150/Hcoord.xvg -- View this message in context: http://gromacs.5086.n6.nabble.com/confusion-about-pdb-file-and-coordinate-xvg-file-tp5005150.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] confusion about pdb file and coordinate.xvg file
Hi all, I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version. I have generated the trajectory file using trjconv utility in gromacs. Using the trr file used to generate the .pdb file, I have generated the co-ordinates of H atoms of water using g_traj utility. I thought I will get the same value of co-ordinates of H atoms in both the files in a particular time step. But it was not so. I am attaching here a part of both the files containing the co-ordinates of H atoms in the first time step. Please note that I have modified and removed the co-ordinates of oxygen atoms from the pdb file. So, Its not exactly the standard format. My doubts are: 1. Am I wrong in thinking that in both the files, co-ordinates of same atoms in a particular time step should be same? 2. If I am wrong, then what is correct ? 3. If I am correct then what may be the possible cause of having different coordinates in both the files? Thanks, Best Regards, Biki Hcoord.xvg (57K) http://gromacs.5086.n6.nabble.com/attachment/5005151/0/Hcoord.xvg traj.pdb (167K) http://gromacs.5086.n6.nabble.com/attachment/5005151/1/traj.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/confusion-about-pdb-file-and-coordinate-xvg-file-tp5005151.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] protein-SWCNT md simulation
On 2/4/13 12:21 AM, Atila Petrosian wrote: Dear Justin Thanks for your reply. 2. Create topology for other elements using g_x2top or other external software and convert them to .itp Can I use PRODRG server to creat topology for cnt? Doubtful. PRODRG produces topologies compatible with Gromos96 43A1 (with manual modification) and doesn't handle periodic molecules, so if you have an infinite CNT, it won't work. You should also base the choice of force field on the quality of its results, not the easy availability of web servers. - Parameters of amber 03 which I used are as follows: ffcnt.atp file CA12.01000 ; sp2 C pure aromatic (benzene) ffcnt.n2t file CCA0.0012.01000 3C 0.141 C 0.141 C 0.141 CCA0.0012.01000 1C 0.141 forcefield.itp file #define _FF_cnt [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 #include ffcntnonbon.itp #include ffcntbon.itp ffcntbon.itp file [ bondtypes ] ; i j funcb0 kb CA CA 10.14000 392459.2 [ angletypes ] ; i j k functh0 cth CA CA CA 1 120.000527.184 [ dihedraltypes ] ; i j k l func phase kd pn CA CA CA CT 4 180.00 4.60240 2 ffcntnonbon.itp file [ atomtypes ] ;name at.num masscharge ptype sigma epsi CA 6 12.010. A 3.39967e-01 3.59824e-01 -- Please check content of these file. If there is problem, please tell me. The problem is in declaring a separate force field for one molecule in the system which, as we have established, is already adequately described by the Amber03 force field that you want to use. I see no need whatsoever to create a new force field, and furthermore one that has fudge values that conflict with the parent. Bottom line in my mind: operate completely within Amber03. -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] steepest descents followed by conjugated gradient
On 2/4/13 4:53 AM, Ruben Cloete wrote: Hi Justin i see lots of papers perform steepest descent followed by conjugated gradients. My question do i use the .gro output file as input to perform conjugated gradient minimization as shown in the commands below? or do i repeat pdb2gmx, editconf and genbox on the trajectory file (protA_em.trr) which i must convert to a .pdb file? There is absolutely no need to reconstruct the entire system, otherwise what was the purpose of the first EM? There are no fixed requirements for file formats; Gromacs can handle just about anything. Use whatever you want. nohup mdrun -s protA_em.tpr -o protA_em.trr -c *protA_b4pr.gro* -g em.log -e em.edr Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 1000 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 754 steps Potential Energy = -6.8864319e+05 Maximum force = 9.1053461e+02 on atom 499 Norm of force = 2.2879843e+01 Now i run conjugated gradient (500 steps) grompp -f em2.mdp -c *protA_b4pr.gro* -p Rv1712.top -o protA_1em.tpr nohup mdrun -s protA_1em.tpr -o protA_em1.trr -c protA_b4pr_1.gro -g em.log -e em.edr when i run these i get an error message segmentation fault? which i know is usually a memory problem. I have no idea why that would happen. The EM from steepest descents seems perfectly reasonable. The seg fault could come from instability within the system, but without a complete .mdp file there is no point in guessing. -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] npt error
On 2/4/13 5:19 AM, Rajalakshmi.C wrote: hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the error message as inner product between old and new vector is 0.0 and water molecules starting at atom 3892 cannot be settled ,check for bad contacts, change the time scale can anyone suggest solution for this . i could not find what the reason will be .i will be waiting for the answer http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] confusion about pdb file and coordinate.xvg file
On 2/4/13 8:06 AM, biki wrote: Hi all, I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version. I have generated the trajectory file using trjconv utility in gromacs. Using the trr file used to generate the .pdb file, I have generated the co-ordinates of H atoms of water using g_traj utility. I thought I will get the same value of co-ordinates of H atoms in both the files in a particular time step. But it was not so. I am attaching here a part of both the files containing the co-ordinates of H atoms in the first time step. Please note that I have modified and removed the co-ordinates of oxygen atoms from the pdb file. So, Its not exactly the standard format. My doubts are: 1. Am I wrong in thinking that in both the files, co-ordinates of same atoms in a particular time step should be same? 2. If I am wrong, then what is correct ? 3. If I am correct then what may be the possible cause of having different coordinates in both the files? The coordinates aren't different in terms of the numbers they actually represent. Gromacs uses nm as a standard unit; PDB files use Angstrom. Note that your numbers are different by exactly a factor of 10. -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] Error in BlueGene
Hello Cíntia, On 02/01/2013 04:19 PM, Cintia C. Vequi-Suplicy wrote: Hello Ricardo, I tried to decrease the integration time but I got the same error. The system is running fine in my local core. I have two questions: 1) What do you mean by I balance the domain decomposition for the larger number of core? When you run at your local hardware, the 8 cores handles your system differently than the 1024, 2048 (or more) cores in bluegene. So you must balance the number of cores with your system size. If you try to run a small system in too many cores, an error may appear: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm So you must decrease their number, or assign different numbers of cores only for PME (mdrun options). There's also the scalability/performance issue 2) Are you running simulations at Bluegene P at Rice University? Yes! Thank you, Cíntia On 30/01/2013 20:48, Ricardo Soares wrote: Hello, before submitting to Bluegene, I always test the system in my local 8 core cpu, and if it works, it will also work in Bluegene, as long as I balance the domain decomposition for the larger number of cores. If your system insists in exploding, even after energy minimization, you could try to decrease the integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in some cases even 0.5 fs. Did you tried that? Cheers, Ricardo. On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote Mark, Thank you for your answer. I did an energy minimization with the file em.mdp (below) and then I did a 40 ns simulation with the same md.mdp I send before. These two steps were done in my local cluster. After that I took the configuration for the simulation in the bluegene and I got these error. I notice that the step that the error occurs depends on the number of nodes I use. I am also including the end of the min.out file. I also tried others integrators for the energy minimization but I always get the same error. Thank you again, Cíntia --- em.mdp integrator = steep tinit= 0.0 dt = 0.002 nsteps = 500 nstcomm = 1 comm-grps= Other SOL nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 100 xtc_precision= 100 xtc-grps = energygrps = Other SOL nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 66 vdw_type = cut-off rvdw = 1.4 DispCorr = No constraints = none --- min.out ... Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 5199 steps, but did not reach the requested Fmax 10. Potential Energy = -1.79302464181879e+06 Maximum force = 6.65022934447791e+02 on atom 22015 Norm of force = 4.90065871184878e+00 gcq#0: Thanx for Using GROMACS - Have a Nice Day --- --- md.mdp file integrator = md tinit= 0.0 dt = 0.002 nsteps = 500 nstcomm = 5 comm-grps= Other SOL nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc_precision= 1000 xtc-grps = energygrps = Other SOL nstlist = 5 ns_type
Re: [gmx-users] Error in BlueGene
Hello David, I think it is the pressure. Because the error starts with the message below. But this only happens in the BlueGene cluster. In my local cluster it is running fine for 60 ns. Thank you, Cintia vol 0.71 imb F 1% vol 0.74 imb F 1% vol 0.73 imb F 1% vol 0.75 imb F 1% vol 0.74 vol 0.75 vol 0.74 vol 0.73 imb F 1% imb F 1% imb F 1% imb F 1% step 3400, will finish Sat Feb 2 08:09:38 2013 vol 0.70 imb F 1% vol 0.75 vol 0.74 vol 0.74 vol 0.74 vol 0.73 imb F 1% imb F 1% imb F 1% imb F 1% imb F 1% vol 0.74 imb F 1% vol 0.73 imb F 1% step 3500, will finish Sat Feb 2 08:07:49 2013 vol 0.73 imb F 1% vol 0.71 imb F 1% vol 0.74 imb F 1% vol 0.74 vol 0.74 imb F 1% vol 0.74 imb F 1% imb F 1% vol 0.75 imb F 1% vol 0.74 imb F 1% step 3600, will finish Sat Feb 2 08:06:01 2013 Warning: 1-4 interaction between 7552 and 7556 at distance 6.386 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 3616 Warning: pressure scaling more than 1%, mu: 1.38174 1.38174 1.4951 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38167 1.38167 1.49502 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38127 1.38127 1.49449 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38206 1.38206 1.49552 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38219 1.38219 1.49569 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38212 1.38212 1.4956 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38215 1.38215 1.49563 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38223 1.38223 1.49573 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38228 1.38228 1.4958 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38227 1.38227 1.49578 Step 3616 Warning: pressure scaling more than 1%, mu: 1.37921 1.37921 1.49181 Step 3616 Warning: pressure scaling more than 1%, mu: 1.3794 1.3794 1.49206 Step 3616 Warning: pressure scaling more than 1%, mu: 1.37967 1.37967 1.49242 Step 3616 Warning: pressure scaling more than 1%, mu: 1.37928 1.37928 1.49191 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38003 1.38003 1.49289 Step 3616 Warning: pressure scaling more than 1%, mu: 1.37973 1.37973 1.4925 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38187 1.38187 1.49527 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38164 1.38164 1.49498 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38183 1.38183 1.49522 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38181 1.38181 1.4952 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38222 1.38222 1.49572 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38229 1.38229 1.49582 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38234 1.38234 1.49588 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38216 1.38216 1.49564 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38221 1.38221 1.49571 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38226 1.38226 1.49578 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38226 1.38226 1.49577 Step 3616 Warning: pressure scaling more than 1%, mu: 1.3822 1.3822 1.4957 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38241 1.38241 1.49597 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38218 1.38218 1.49568 Step 3616 Warning: pressure scaling more than 1%, mu: 1.3822 1.3822 1.4957 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38213 1.38213 1.49561 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38213 1.38213 1.49561 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38221 1.38221 1.49571 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38222 1.38222 1.49573 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38229 1.38229 1.49581 Step 3616 Warning: pressure scaling more than 1%, mu: 1.37951 1.37951 1.49221 Step 3616 Warning: pressure scaling more than 1%, mu: 1.3815 1.3815 1.49479 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38153 1.38153 1.49483 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38153 1.38153 1.49483 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38215 1.38215 1.49564 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38225 1.38225 1.49576 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38228 1.38228 1.4958 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38226 1.38226 1.49577 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38216 1.38216 1.49565 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38229 1.38229 1.49581 Step 3616 Warning: pressure scaling more than 1%, mu: 1.3823 1.3823 1.49582 Step 3616 Warning: pressure scaling more than 1%, mu: 1.38226 1.38226 1.49578 Step 3616 Warning: pressure
[gmx-users] Re: confusion about pdb file and coordinate.xvg file
Thanks Justin for your reply. -- View this message in context: http://gromacs.5086.n6.nabble.com/confusion-about-pdb-file-and-coordinate-xvg-file-tp5005151p5005163.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] system far from the equilibration state
Hi, I am simulating a system of peptide/membrane/water. If my system is far from the equilibration, would that be correct if I use Berendsen pressure coupling for nano seconds to do NPT equilibration and then change it to Parrinello-Rahman to get the true pressure? Anybody may suggest me please? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dummy/ghost atom - regd
Dear Gromacs users, I am planing to have a reference atom(non-bonded) in my system, whose position will not change during simulations and shouldn't feel/exert any force from/on the other atoms(ghost atom). How can I do this in gromacs ? can I set electrostatic and van der waals parameters to zero ? or is there any efficient way to do this ? Any help will be highly appreciated. Regards, Ramesh. -- 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] system far from the equilibration state
On 2/4/13 2:04 PM, Shima Arasteh wrote: Hi, I am simulating a system of peptide/membrane/water. If my system is far from the equilibration, would that be correct if I use Berendsen pressure coupling for nano seconds to do NPT equilibration and then change it to Parrinello-Rahman to get the true pressure? Anybody may suggest me please? Sounds reasonable. Berendsen is a useful method in such cases. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs-4.6.tar.gz installation question
On 2/4/13 3:30 PM, jeela keel wrote: *Dear All, I am trying to install gromacs, I dowloaded **gromacs-4.6.tar.gzftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gzand following the instruction in the following website http://www.gromacs.org/Documentation/Installation_Instructions#4._Doing_a_build_of_GROMACS I read the instraction but I am still kind of confused. Do I need to download both FFTW and CMake or just choose one of them for the gromacs installation? Both. FFTW is used for Fourier transforms. CMake is the compiler that builds the software. Also can I use FTTW **fftw-2.1.5.tar.gzftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gzinstead of **fftw-3.3.3.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3.tar.gz becuase I also want to download Lammps in my computer that can only use fftw 2.1.5 We always advise using the newest version. There is no problem at all in maintaining different versions in different locations. -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: gromacs-4.6.tar.gz installation question
Thank you for your respond but I did not get the respond to my email, I found the answer on-line. I don't know why I am not receiving any email back from the mailing list. Thank you Jeela On Mon, Feb 4, 2013 at 12:30 PM, jeela keel jeel...@gmail.com wrote: *Dear All, I am trying to install gromacs, I dowloaded **gromacs-4.6.tar.gzftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gzand following the instruction in the following website http://www.gromacs.org/Documentation/Installation_Instructions#4._Doing_a_build_of_GROMACS I read the instraction but I am still kind of confused. Do I need to download both FFTW and CMake or just choose one of them for the gromacs installation? Also can I use FTTW **fftw-2.1.5.tar.gzftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gzinstead of **fftw-3.3.3.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3.tar.gzbecuase I also want to download Lammps in my computer that can only use fftw 2.1.5 Thank you fro your help Jeela * -- 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] Protein unfolded after COM pulling
On 2/4/13 9:32 PM, Yun Shi wrote: Hi all, I am pulling one monomer of a tetrameric protein away from the other three monomers with pull_k1 = 1 and pull_rate1 = 0.0005. As shown in the attached picture, the green monomer (being pulled) has unfolded while two regions on it are still interacting with the other three monomers at the end of my pulling simulations (13 ns, so COM distance has been pulled 6.5 nm). Attachments to the list are prohibited; if you have files or images to share you must provide a URL. If I want to calculate deltaG of this process, can I use distance restraints on the green monomer being pulled to maintain its folded structure? Otherwise, I will have to construct a larger box or pull even slower than 0.5 nm/ns. Yes, you probably need distance restraints. Complex restraints often fail with domain decomposition, so you may need to use particle decomposition instead. -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] Membrane simulation - error during EM after inflation step
Hello Justin, Thank you for providing a tutorial for membrane simulation. I am doing membrane simulation by following your tutorial. When I tried to do energy minimization after inflating the system i got the following result. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.6157550e+17 Maximum force =inf on atom 2093 Norm of force =inf So the system is not converged well. I checked the output .gro file the protein came completely out of the bilayer. I tried to fix the problem by increasing the -fc value to 100 but still problem continues. Will you please tell me what will be the reason behind this problem and how to fix it. Thank you John K -- View this message in context: http://gromacs.5086.n6.nabble.com/Membrane-simulation-error-during-EM-after-inflation-step-tp5005177.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] Regarding manual velocity generation in simulation
Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. -- *--- 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
