[gmx-users] Re: Umbrella sampling with large pulling distance (larger than half of the box size) (Thomas Schlesier)
-- Message: 1 Date: Wed, 20 Mar 2013 12:55:45 +0100 From: Thomas Schlesier schl...@uni-mainz.de Subject: [gmx-users] Umbrella sampling with large pulling distance (larger than half of the box size) To: gmx-users@gromacs.org Message-ID: 5149a3c1.2000...@uni-mainz.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Look for pull_geometry = direction_periodic This should solve the problem. Greetings Thomas Thanks very much for your reply. However, I want to use Umbrella sampling to get the potential of mean force curve with g_wham. As I know, pull_geometry = direction cannot do that, so as direction_periodic? Am 20.03.2013 12:00, schrieb gmx-users-requ...@gromacs.org: Dear all, I want to use Umbrella sampling method to calculate the potential of mean force. Unfortunately, the distance of my two groups is very large (about 10nm, larger than the half of simulation box size 16nm). Without increasing the box size (too large!!), is there any ideas to solve this problem? In another way, is it possible to modify the pulling code (pull.c) to force the umbrella sampling method only calculate the distance of the groups in the box but not the periodic image? -- -- 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 Blue Gene/Q is so slow?
Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone tell me what's wrong in my simulation? Any suggestion will be appreciated. Following is my md.mdp file: constraints= hbonds constraint_algorithm = LINCS lincs_order= 4 comm_mode = Angular comm_grps = system integrator = sd ;annealing = single single ;annealing_npoints = 2 2 ;annealing_time = 0 500 0 500 ;annealing_temp = 200 300 200 300 dt = 0.002 ; ps ! nsteps = 500 ; total 5000 ps. nstcomm= 10 nstcalcenergy = 10 nstxout= 1 ; collect data every 1 ps nstenergy = 1 nstvout= 1 nstlog = 1000 ;nstxtcout = 5 ;xtc_grps = system nstfout= 0 nstlist= 10 ns_type= grid pbc= no rlist = 1.2 coulombtype= cut-off rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;energygrps = alpha1 alpha2 alpha3 beta1 beta2 beta3 gamma ;DispCorr = EnerPres ; Berendsen temperature coupling is on in two groups Tcoupl = tau_t = 0.5 tc-grps= system ref_t = 300 ; Pressure coupling is on Pcoupl = no ;berendsen tau_p = 1.0 compressibility= 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel= yes gen_temp = 300 gen_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 1.2 sa_surface_tension = 2.25936 Here is the preformace info: M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops - Generalized Born Coulomb61.4828922951.179 0.4 GB Coulomb + LJ 2565.481100 156494.34719.4 Outer nonbonded loop 152.2685461522.685 0.2 1,4 nonbonded interactions 116.143224 10452.890 1.3 Born radii (HCT/OBC) 2868.34 524884.66964.9 Born force chain rule 2868.34 43023.334 5.3 NS-Pairs 516.814696 10853.109 1.3 Reset In Box 4.464788 13.394 0.0 CG-CoM 4.482576 13.448 0.0 Bonds 22.1744341308.292 0.2 Angles 80.586114 13538.467 1.7 Propers160.742142 36809.951 4.6 Virial 4.636254 83.453 0.0 Update 44.4788941378.846 0.2 Stop-CM 4.455894 44.559 0.0 Calc-Ekin 44.4877881201.170 0.1 Lincs 44.9516302697.098 0.3 Lincs-Mat 261.8225521047.290 0.1 Constraint-V44.951630 359.613 0.0 Constraint-Vir 2.251163 54.028 0.0 - Total 808731.820 100.0 - D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 660.5 av. #atoms communicated per step for LINCS: 2 x 34.3 Average load imbalance: 1.7 % Part of the total run time spent waiting due to load imbalance: 1.4 % R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 8502 59.421 37.1 0.5 DD comm. load 8 80.0040.0 0.0 Comm. coord. 8 5001 16.575 10.4 0.2 Neighbor
[gmx-users] Re: Re: why Blue Gene/Q is so slow? (Mark Abraham)
-- Message: 8 Date: Tue, 17 Jul 2012 18:40:05 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] why Blue Gene/Q is so slow? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 500524e5.9050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 17/07/2012 5:00 PM, DeChang Li wrote: Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone tell me what's wrong in my simulation? Any suggestion will be appreciated. Your workstation is running highly effective optimized SSE loops. BlueGene/Q is not using its multiple FPU because that code hasn't been written (for explicit or implicit solvation), and BlueGene's processors are probably slower too. Mark That means the code itself causes only 10% speed in BlueGene/Q compared with intel CPUs workstation? Is there any method to improve the speed in BG/Q? Dechang Following is my md.mdp file: constraints= hbonds constraint_algorithm = LINCS lincs_order= 4 comm_mode = Angular comm_grps = system integrator = sd ;annealing = single single ;annealing_npoints = 2 2 ;annealing_time = 0 500 0 500 ;annealing_temp = 200 300 200 300 dt = 0.002 ; ps ! nsteps = 500 ; total 5000 ps. nstcomm= 10 nstcalcenergy = 10 nstxout= 1 ; collect data every 1 ps nstenergy = 1 nstvout= 1 nstlog = 1000 ;nstxtcout = 5 ;xtc_grps = system nstfout= 0 nstlist= 10 ns_type= grid pbc= no rlist = 1.2 coulombtype= cut-off rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;energygrps = alpha1 alpha2 alpha3 beta1 beta2 beta3 gamma ;DispCorr = EnerPres ; Berendsen temperature coupling is on in two groups Tcoupl = tau_t = 0.5 tc-grps= system ref_t = 300 ; Pressure coupling is on Pcoupl = no ;berendsen tau_p = 1.0 compressibility= 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel= yes gen_temp = 300 gen_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 1.2 sa_surface_tension = 2.25936 Here is the preformace info: M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops - Generalized Born Coulomb61.4828922951.179 0.4 GB Coulomb + LJ 2565.481100 156494.34719.4 Outer nonbonded loop 152.2685461522.685 0.2 1,4 nonbonded interactions 116.143224 10452.890 1.3 Born radii (HCT/OBC) 2868.34 524884.66964.9 Born force chain rule 2868.34 43023.334 5.3 NS-Pairs 516.814696 10853.109 1.3 Reset In Box 4.464788 13.394 0.0 CG-CoM 4.482576 13.448 0.0 Bonds 22.1744341308.292 0.2 Angles 80.586114 13538.467 1.7 Propers160.742142 36809.951 4.6 Virial 4.636254 83.453 0.0 Update 44.4788941378.846 0.2 Stop-CM 4.455894 44.559 0.0 Calc-Ekin 44.4877881201.170 0.1 Lincs 44.9516302697.098 0.3 Lincs-Mat 261.8225521047.290 0.1 Constraint-V44.951630 359.613 0.0 Constraint-Vir 2.251163 54.028 0.0
[gmx-users] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )
Dear all, I want to calculate the ion solvation free energy (e.g. an ion Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR) method, following the tutorial by Justin A. Lemkul. However, if I turn off the Coulombic interaction, the total charge of my system would not neutral at all. Does this affact my calculation? = Dechang Li , Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace Engineering Beijing Institute of Technology Beijing 100081, P. R. China = -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can Gromacs do Targeted MD simulation?
Hi all, Just as the title, can Gromacs do Targeted MD simulations? If Yes, how to set up the simulation procedure? -- 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] How to exclude the interactions between molecule A and B in Gromacs?
Dear all, I want to use Gromacs to run an enhanced sampling molecular dynamics (ESMD) proposed by Karplus’s group (J. Am. Chem. Soc. (1990) 112, 9161-9175. J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to exclude the interactions (especially the Coulomb interactions) between some small molecules (e.g. ligand A and its replica). How can Gromacs to do this? Any suggestion will be very appreciated. Best regards, = Dechang Li, Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace Engineering Beijing Institute of Technology Beijing 100081, P. R. China = -- 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] distance VS. direction option in Umbrella sampling, in Gromacs 4.0
Dear all, What is the difference between the option Distance and Direction in Umbrella Sampling? In my opinion, the option Direction means that pulling the pull_group1 through the direction related to the reference group. Right? But how about the option Distance? -- 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: distance VS. direction option in Umbrella sampling, in Gromacs 4.0 (Justin A. Lemkul)
-- Message: 2 Date: Tue, 16 Nov 2010 08:01:42 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] distance VS. direction option in Umbrella sampling, in Gromacs 4.0 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ce280b6.2080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed DeChang Li wrote: Dear all, What is the difference between the option Distance and Direction in Umbrella Sampling? In my opinion, the option Direction means that pulling the pull_group1 through the direction related to the reference group. Right? But how about the option Distance? There was some discussion about this previously, so do search the archives. If memory serves, distance does not allow negative relative displacements, while any of the other pull methods do. The distance method is most applicable when pulling such that the COM distance always increases, or remains positive throughout the process. Also, from an application perspective, the .mdp file options are different (direction + pull_vec1, distance + pull_dim). Does mean that when using distance + pull_dim (if using pull_dim = Y Y Y), the pull force vector is pointing from the reference group to the pull group? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Umbrella sampling with temperature and pressure coupling method problem
Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- 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: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)
Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Umbrella sampling with temperature and pressurecoupling method problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cbd9d87.6080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed chris.ne...@utoronto.ca wrote: Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but probably you need to provide more information to get a useful answer there. The Berendsen barostat suffers from the same limitations as the thermostat - the pressure distribution does not produce a true NPT ensemble. Whether the correct canonical ensemble (NPT or NVT) is important (or indispensable) for umbrella sampling? If I used the weak coupling method (Berendsen) to do the simulations, can I extract the PMF from the umbrella sampling simulations? -Justin -- original message -- Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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: Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul) (Justin A. Lemkul)
Message: 5 Date: Tue, 19 Oct 2010 13:06:42 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and pressurecoupling method problem (Justin A. Lemkul) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cbdd022.6020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed DeChang Li wrote: Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Umbrella sampling with temperature and pressurecoupling method problem To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4cbd9d87.6080...@vt.edu mailto:4cbd9d87.6080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but probably you need to provide more information to get a useful answer there. The Berendsen barostat suffers from the same limitations as the thermostat - the pressure distribution does not produce a true NPT ensemble. Whether the correct canonical ensemble (NPT or NVT) is important (or indispensable) for umbrella sampling? If I used the weak coupling method (Berendsen) to do the simulations, can I extract the PMF from the umbrella sampling simulations? I would think that a proper statistical mechanical ensemble would be considered indispensable for any simulation. In my mind, there is no real reason to use less accurate methods when collecting data. If your goal is a comparison of methods, or consistency with other results, sure, then you may have a reason to use algorithms that may be less than optimal. For any sensitive thermodynamic study, I would strongly argue that your potential energy surface needs to be rigorously correct. The point is this. You have to defend your choices to a skeptical audience (reviewers). This is one question that might be asked, and really should be. Methods should be scrutinized. So I would ask you this: why perform your simulations with algorithms that are not as accurate as others, when those better algorithms are accessible to you and do not harm performance in any demonstrable way? -Justin Thank you for your reply! So I will use Nose-Hoover for temperature coupling and Parrinello-Rahman for pressure coupling in the data collection. Anyway, I may do some simulations with Berendsen method to see if there is any difference in results when using the two coupling methods. -Justin -- original message -- Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 the option pull_dim
Dear all, Does the following three options do the same things in the pull code of Gromacs 4.0: 1. pull_dim = Y Y Y pull_vec1 = 1 0 0 ** 2. pull_dim = Y N N pull_vec1 = 1 0 0 ** 3. pull_dim = Y N N pull_vec1 = 1 0.5 0.5 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] what is the eigenvalue unit in Gromacs?
Dear all, I used g_nmeig to diagonalize the Hessian matrix, that I got the eigenvalues. However, I found that in the file 'eigenval.xvg' the unit of the eigenvalues are Eigenvalue [Gromacs units]. What is the '[Gromacs units]'? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] the code speed between Gromacs 3.0 and Gromacs 4.0
Dear gmx-users, Are there any comparisons of the code speed between Gromacs 3.0 and Gromacs 4.0. In my calculation, I got a speed about 3.5ns/day of a system have about 50,000 atoms, using 8 CPUs with Gromacs 3.3.1. In contrast, the speed can reach up to 7.3ns/day when switch to Gromacs 4.0.7 while the other conditions are keep the same. Is this result normal? Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How to calculate the lifetime of one hydrogen bond
Dear all, I want to calculate the lifetime of one hydrogen bond. I used g_hbond to do this. Here is the out put: Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward-0.001 -1750.289-666.000 Backward -0.001 -930.928-666.000 One-way 0.000 6622.058 26.338 Integral0.001739.899 20.905 Relaxation 0.778 1.286 5.152 Which is the lifetime of the hydrogen bond? What does the Forward, Backward etc. mean? Best regards, 2009-1030 = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Different RMSD of the same system
Dear all, I have did a simulation with explict water model using Gromacs-3.3.3. To save the hard disk space, I didn't collect the coordinates of water by using the following parameters: dt = 0.002 ; ps ! nsteps = 3000 ; total time. nstcomm= 1 nstxout= 3000 ; nstenergy = 1000 nstvout= 3000 nstlog = 2 nstxtcout = 1000 xtc_grps = Protein In addition, I did a short simulation of the system in which the coordinates of water were collected every 2 ps. For comparison, I calculated the RMSD of C-alpha atoms of the protein. However, the values are different of the two systems! Are these differences reasonable? BTW: I didn't generate the velocities in the beginning. RMSD of C-alpha atoms without collecting water coordinates: @ subtitle C-alpha after lsq fit to C-alpha 0.0000.0001220 2.0000.0545500 4.0000.0691709 6.0050.0657938 8.0000.0723884 10.0000.0800556 12.0100.0745629 14.0100.0732903 16.0000.0752474 18.0000.0774800 20.0000.0914096 22.0190.0981914 24.0190.0983810 26.0190.1057151 28.0190.1053288 30.0190.1084988 RMSD of C-alpha atoms with collecting water coordinates: @ subtitle C-alpha after lsq fit to C-alpha 0.0000.0002658 2.0000.0569104 4.0000.0642647 6.0050.0673439 8.0000.0760661 10.0000.0837568 12.0100.0978260 14.0100.1037093 16.0000.1087546 18.0000.1126641 20.0000.1321630 22.0190.1270466 24.0190.1102782 26.0190.1115073 28.0190.1304575 30.0190.1173159 Best regards, = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: force field parameter for ligands
Message: 1 Date: Mon, 25 May 2009 01:15:44 -0700 From: Zhanglin Ni z...@u.washington.edu Subject: [gmx-users] force field parameter for ligands To: gmx-users@gromacs.org Message-ID: 009701c9dd11$012c1ae0$0301a...@zn3 Content-Type: text/plain; format=flowed; charset=iso-8859-1; reply-type=original Dear all, where do you usually get topolgy for small molecule ligand or do it manually? Dundee PRODRG Server seems to be capable of making .top for ffgmx only but not new ones like ffG53a6,etc. Thanks I think the AMBER tools antechamber will be helpful. Johnny -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 61, Issue 120 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] the vdw and electrostatic energy
Dear all, When we do a MD simulation, we always set a cutoff of non-bonded interactions, e.g. r=1.2 nm. When the simulation finished, we can use the command g_energy -f ener.edr -s ... to abtain the non-boned energy of the system. My question is whether the non-bonded energy values dependent on the non-bonded cutoff? If YES, there may be no problem of the vdw interaction (LJ-SR), because the vdw interaction vanish in a short distance. But how about the electrostatic term with the distance dependence of 1/r^2 ? Best regards, = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re:Re: the vdw and electrostatic energy (Ran Friedman)
-- Message: 3 Date: Thu, 16 Apr 2009 14:11:51 +0200 From: Ran Friedman r.fried...@bioc.uzh.ch Subject: Re: [gmx-users] the vdw and electrostatic energy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49e72087.8020...@bioc.uzh.ch Content-Type: text/plain; charset=GB2312 Hi, This problem has been discussed for decades in the literature. There are approaches such as PME and reaction field to deal with the long-range electrostatics. I did not mean that. I want to know that when we use g_energy in Gromacs to read the energy from the file ener.edr, does the cutoff affect the values of the energy? For example, when the cutoff is set to 1.2 nm and the PME method is used, does the energy term Coul-SR read by g_energy contain the long range part ? Ran. Dechang Li wrote: Dear all, When we do a MD simulation, we always set a cutoff of non-bonded interactions, e.g. r=1.2 nm. When the simulation finished, we can use the command g_energy -f ener.edr -s ... to abtain the non-boned energy of the system. My question is whether the non-bonded energy values dependent on the non-bonded cutoff? If YES, there may be no problem of the vdw interaction (LJ-SR), because the vdw interaction vanish in a short distance. But how about the electrostatic term with the distance dependence of 1/r^2 ? Best regards, = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How VMD to display the velocity
Dear all, Is there any methods to display the velocity of the atoms using VMD? I saw that in the .gro file, it contains six columns. The last columns are the vector of the velocity. Can I display the velocity in VMD using arrows, with which the orientation and the magnitude can be displayed by the arrowhead and the length of the arrows? If NO, how can I do this work with other package? Thanks in advance! Best regards, 2009-3-5 = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] eigenvec.trr and eigenval.xvg
Dear all, I used g_covar and g_anaeig to generate the eigenvectors of a trajectory. In the eigenvec.trr (I converted it to .gro file) file, the first, second and third eigenvectors showed that: The first: Generated by trjconv : in water t= -1.0 The second: Generated by trjconv : in water t= 0.0 The third: Generated by trjconv : in water t= 2.13704 But I saw in the eigenval.xvg file that the eigenvalues are : 1 2.13704 2 0.492212 3 0.308174 What do the first and second eigenvectors mean? The related eigenvalues are -1 and 0 ? Best regards, 2009-3-5 = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] generalized order parameters S2
Dear all, I have run a 100ns simulation of protein. I want to calculate the generalized order parameters S2 for N-H. It was said that to calculate S2, the overall motion should be subtracted first. How can I subtract the overall motion? Can I use the command 'trjconv' to fit the protein to a reference strucutre firstly, and then calculate S2 using command 'g_rotacf'? If YES, what the reference structure is? The average structure in the trajectory? Best regards, 2009-3-3 = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_rotacf, order parameter S2 problem
Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling that the order parameter is negative! Here is one of my results: @title Rotational Correlation Function @xaxis label Time (ps) @yaxis label C(t) @TYPE xy ... 119944.000-0.16902 119946.000-0.16845 119948.000-0.16812 119950.000-0.16845 119952.000-0.16834 119954.000-0.16825 119956.000-0.16875 119958.000-0.16823 119960.000-0.16850 119962.000-0.16885 119964.000-0.16892 119966.000-0.16924 119968.000-0.16885 119970.000-0.16928 119972.000-0.16889 119974.000-0.16901 119976.000-0.16866 119978.000-0.16901 119980.000-0.16895 119982.000-0.16953 119984.000-0.16932 119986.000-0.16961 119988.000-0.16947 119990.000-0.16890 119992.000-0.16952 119994.000-0.16986 119996.000-0.16970 119998.000-0.16941 12.000-0.16908 The command I used is : g_rotacf -s Order.tpr -f Order.trr -d -n index.ndx -P 2 -nice 0 . Actually, when I used the option -P 1, the negative results appear similarly. Before I calculated the S2 parameter, I removed the rotation and translation movement of the molecule using the tool trjconv. Is that the negative results reasonable? Best regards, 2009-1-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole)
Dechang Li wrote: Dear all, I want to use g_rotacf to calculate the order parameter(S2, N-H bond in main chian). The tool g_rotacf needs an index.ndx file that contains two vectors. g_rotacf wants the index number of two atoms to calculate the order parameter of an NH vector. You should give the index number of the atoms N and H and use the option -d. Note that you have to take care of the overall rotation of the molecule in the calculation. Either you remove it before the calculation or you include it in the fit of the correlation function. I read the manual that the index file should contain 3 atoms, i.e. (i, j, k). Is that mean I should write the index file like this: [ group1 ] 1 3 4 [ group2 ] 5 8 9 where 1 for atom Ca, 3 for atom N, and 4 for atom H, in a peptide? This will not define a vector! To follow the movement of the NH vector (made of two atoms! the N and the H) you need only two index numbers, the one of the N and the one of the H. Then the option -d is needed for g_rotacf to treat the corresponding vector. Thank you for your reply! It was helpful. It was said that the index file only need 2 atoms, i.e. index of N and H. However, for the residue PRO, how to define the vector NH? How can I make the index.ndx file? Can I use the tool make_ndx to do this? Or I need to write the file manually? See http://wiki.gromacs.org/index.php/Index_File. I think you just want to write a file by hand. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole)
Message: 4 Date: Sun, 04 Jan 2009 14:52:47 +0100 From: Xavier Periole x.peri...@rug.nl Subject: Re: [gmx-users] calculation of the order parameter S2 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: web-103138...@mail3.rug.nl Content-Type: text/plain;charset=utf-8;format=flowed On Sun, 04 Jan 2009 13:38:33 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: Dechang Li wrote: Dear all, I want to use g_rotacf to calculate the order parameter(S2, N-H bond in main chian). The tool g_rotacf needs an index.ndx file that contains two vectors. g_rotacf wants the index number of two atoms to calculate the order parameter of an NH vector. You should give the index number of the atoms N and H and use the option -d. Note that you have to take care of the overall rotation of the molecule in the calculation. Either you remove it before the calculation or you include it in the fit of the correlation function. I read the manual that the index file should contain 3 atoms, i.e. (i, j, k). Is that mean I should write the index file like this: [ group1 ] 1 3 4 [ group2 ] 5 8 9 where 1 for atom Ca, 3 for atom N, and 4 for atom H, in a peptide? How can I make the index.ndx file? Can I use the tool make_ndx to do this? Or I need to write the file manually? See http://wiki.gromacs.org/index.php/Index_File. I think you just want to write a file by hand. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 57, Issue 4 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] S2Min and S2Max
Dear all, After running the g_chi, a file named as order.xvg is generated. In this file, I found that there are S2min and S2max values for each amino acid residue. What is the difference between S2 min and max? Here is part of my order.xvg @ s0 legend S2Min @ s1 legend S2Max @ s2 legend Phi @ s3 legend Psi @ s4 legend Omega #Res. S2Min S2MaxPhiPsi Omega 1 0.833 0.871 0.871 0.833 0.000 2 0.746 0.974 0.746 0.938 0.974 3 0.909 0.977 0.961 0.909 0.977 4 0.902 0.975 0.902 0.969 0.975 5 0.965 0.980 0.965 0.980 0.978 6 0.960 0.977 0.977 0.960 0.973 7 0.945 0.977 0.945 0.977 0.975 8 0.971 0.976 0.975 0.971 0.976 9 0.877 0.983 0.983 0.877 0.977 10 0.855 0.976 0.855 0.963 0.976 11 0.923 0.978 0.977 0.923 0.978 12 0.831 0.974 0.831 0.967 0.974 Thanks alot!!! Best regards, 2009-1-3 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: li.d...@gmail.com = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] calculation of the order parameter S2
Dear all, I want to use g_rotacf to calculate the order parameter(S2, N-H bond in main chian). The tool g_rotacf needs an index.ndx file that contains two vectors. How can I make the index.ndx file? Can I use the tool make_ndx to do this? Or I need to write the file manually? Best regards, 2009-1-4 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: li.d...@gmail.com = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] questions about g_hbond
Dear all, I used g_hbond to count the number of hydrogen bonds between two molecules. The result was here: # g_hbond_mpi is part of G R O M A C S: # # GROningen MAchine for Chemical Simulation # @title Hydrogen Bonds @xaxis label Time @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 15 8 2 12 11 4 12 14 6 16 8 8 14 15 10 15 9 12 16 6 14 12 13 16 13 5 18 11 11 WHY the number in third column sometimes smaller than the number in second column? Best regards, = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] system contains proteins and DNAs with ffamber99
Dear all, Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can Gromacs add the hydrogen atoms of the water molecules? Additionly, when use Gromacs with the force field ffamber99, Can it add the hydrogen atoms of the DNA? Can I use the force field ffamber99 to simulate the system which contains proteins and DNAs? Best regards, = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_hbond distance distribution problem
-- Message: 4 Date: Sun, 18 May 2008 00:50:30 +0200 From: Xavier Periole [EMAIL PROTECTED] Subject: Re: [gmx-users] g_hbond distance distribution problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=utf-8;format=flowed Dechang Li wrote: Dear all, I used command g_hbond to calculated the distance distribution of hbonds in my system. There are two columns in the file hbdist.xvg, as showed follow: @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 .. ... I think the second column is the distance distribution of hbonds, so the summation of the second column should be 1, right? However, the summation in my file is 200, what is the problem? The sum itself should not be one but the integral of the curve should be one. Considering the bin you have the 200 makes sense. Try to integrate. Could be, then it is ot normalized. You can do that easily in xmgrace. I integrated it, the result is 1.0 exactly. And the first column refered to Hydrogen - Acceptor Distance (nm) , should it be the distance of donors and acceptor? Am I right? At what position is the top of the distribution? If it is at 0.17 nm it is HA as it says. The top of the distribution is about 0.3 nm, so it is the D-A distance? Best regards, 2008-5-17 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_hbond distance distribution problem
Dear all, I used command g_hbond to calculated the distance distribution of hbonds in my system. There are two columns in the file hbdist.xvg, as showed follow: @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 .. ... I think the second column is the distance distribution of hbonds, so the summation of the second column should be 1, right? However, the summation in my file is 200, what is the problem? And the first column refered to Hydrogen - Acceptor Distance (nm) , should it be the distance of donors and acceptor? Am I right? Best regards, 2008-5-17 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: the number of water molecules (Jian Zou)
Message: 2 Date: Mon, 21 Apr 2008 10:43:27 -0400 From: Jian Zou [EMAIL PROTECTED] Subject: [gmx-users] Re: the number of water molecules To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 How about using vmd selection within to do this I have tried this. However, vmd can tell me the number in this frame, but there are about 5000 frames! I am tring to write a script to let vmd explore the results to a file VS. frames. If I make any progress, let you know. ^_^ Message: 3 Date: Sun, 20 Apr 2008 21:01:57 +0800 From: Dechang Li [EMAIL PROTECTED] Subject: [gmx-users] the number of water molecules To: gmx-users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=gb2312 Dear all, How can I calculate the number of water molecules around the protein with a distance about 5 angstrom? Is that possible in Gromacs? Best regards, 2008-4-20 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the number of water molecules
Dear all, How can I calculate the number of water molecules around the protein with a distance about 5 angstrom? Is that possible in Gromacs? Best regards, 2008-4-20 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham)
gmx-users-request,您好！ Message: 1 Date: Sat, 5 Apr 2008 11:48:15 +0800 From: DeChang Li [EMAIL PROTECTED] Subject: [gmx-users] RMSD VS. parallel simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. Best regards, 2008-4-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = -- Message: 2 Date: Sat, 05 Apr 2008 14:02:29 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] RMSD VS. parallel simulation To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed DeChang Li wrote: Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? MD allows you to observe an ensemble (usually at or approaching equilibrium) over time. Any single point of that time isn't any more significant than any other. So you should expect any pair of points in different simulations (which had their velocities generated with different random numbers, right?) to generally give different values for observables, and for that not to mean anything much. Distributions of observables over long enough periods of time should be the same, however. I have done the two simulation last 1 ns long. For the last 500ps, the RMSD of the protein is 0.21nm (0.016nm) in the 16 CPUs simulation, but 0.15nm (0.011nm) in the 2 CPUs simulaiton, respectively. (The value in parentheses reflects the standard deviation). I think at the last 500ps the system should be equilibrium. Why the RMSD so different? Does it mean I should simulate much longer? These numbers don't mean anything out of context. Even the most stable protein structure of a thousand residues might have an all-atom average RMSD of this size. In a decapeptide it might mean there isn't a single conformer, or that equilibrium is not yet reached. In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. If you've done an equilibration or EM, the structure can have changed during that. I mean the initial structure is the structure I used to generate the .tpr file for mdrun_mpi. What were your command lines, choices for groups and outputs? The most likely simple explanation is that you haven't done what you think you've done :-) My command lines: g_rms -s md.tpr -f md.trr -o rms_protein.xvg -n index.ndx choices for groups: Select group for least squares fit: Protein Select group for RMSD calculation: Protein Mark -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: RMSD VS. parallel simulation
Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. RMSD VS. parallel simulation (DeChang Li) 2. Re: RMSD VS. parallel simulation (Mark Abraham) -- Message: 1 Date: Sat, 5 Apr 2008 11:48:15 +0800 From: DeChang Li [EMAIL PROTECTED] Subject: [gmx-users] RMSD VS. parallel simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. Best regards, 2008-4-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = -- Message: 2 Date: Sat, 05 Apr 2008 14:02:29 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] RMSD VS. parallel simulation To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed DeChang Li wrote: Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? MD allows you to observe an ensemble (usually at or approaching equilibrium) over time. Any single point of that time isn't any more significant than any other. So you should expect any pair of points in different simulations (which had their velocities generated with different random numbers, right?) to generally give different values for observables, and for that not to mean anything much. Distributions of observables over long enough periods of time should be the same, however. I have done the two simulation last 1 ns long. For the last 500ps, the RMSD of the protein is 0.21nm (0.016nm) in the 16 CPUs simulation, but 0.15nm (0.011nm) in the 2 CPUs simulaiton, respectively. (The value in parentheses reflects the standard deviation). I think at the last 500ps the system should be equilibrium. Why the RMSD so different? Does it mean I should simulate much longer? In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. If you've done an equilibration or EM, the structure can have changed during that. I mean the initial structure is the structure I used to generate the .tpr file for mdrun_mpi. Mark -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 48, Issue 12 * = = = = = = = = = = = = = = = = = = = = 致 礼！ Dechang Li [EMAIL PROTECTED] 2008-04-05 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RMSD VS. parallel simulation
Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. Best regards, 2008-4-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] different results when using different number cpus
Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Grid: 19 x 14 x 14 cells
Dear all, During my simulation, in the md.log file there always appeared Grid: 19 x 14 x 14 cells Grid: 18 x 14 x 14 cells Grid: 19 x 14 x 14 cells Grid: 18 x 14 x 14 cells Grid: 19 x 14 x 14 cells Grid: 18 x 14 x 14 cells Grid: 19 x 14 x 14 cells What did it mean? Best regards, 2007-12-2 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Incomplete header: nr 3078 time 9408
Dear all, I used Gromacs-3.3.1 to do a simulation. When it finished, I used command g_dist to calculate two groups distance VS time. But at time 9408ps, it stopped and showed Incomplete header: nr 3078 time 9408. My simulation is 12ns longer. What is the problem? How can I resolve it? Best regards, 2007-11-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:Re: Incomplete header: nr 3078 time 9408
Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Incomplete header: nr 3078 time 9408 (David van der Spoel) 2. Re: trjorder does not write trajectory file (Dmytro Kovalskyy) -- Message: 1 Date: Sun, 11 Nov 2007 09:41:35 +0100 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Incomplete header: nr 3078 time 9408 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8; format=flowed Dechang Li wrote: Dear all, I used Gromacs-3.3.1 to do a simulation. When it finished, I used command g_dist to calculate two groups distance VS time. But at time 9408ps, it stopped and showed Incomplete header: nr 3078 time 9408. My simulation is 12ns longer. What is the problem? How can I resolve it? start by testing the trajectory with gmxcheck I did what you said. Following is the message: Reading frame3000 time 9254.000 Warning at frame 3077. Velocities for atom 11896 are large (52568.4) Warning at frame 3077. Velocities for atom 11896 are large (7.68295e+31) Warning at frame 3077. Velocities for atom 11896 are large (2.75578e+23) Warning at frame 3077. Velocities for atom 11901 are large (9410) WARNING: Incomplete header: nr 3078 time 9408 Item#frames Timestep (ps) Step 30782 Time 30782 Lambda30782 Coords30782 Velocities30782 Forces 0 Box 30782 Did it mean my simulation was failed? But I have checked the energy file ener.edr, too. The energy file seems fine. How did it happen? Can I use the date after time 9254ps? Best regards, 2007-11-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =��� ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- Message: 2 Date: Sun, 11 Nov 2007 13:01:19 +0200 (EET) From: Dmytro Kovalskyy [EMAIL PROTECTED] Subject: Re: [gmx-users] trjorder does not write trajectory file To: Justin A. Lemkul [EMAIL PROTECTED] Cc: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=utf-8 It works fine for me under 3.3.1 - what command line are you issuing? trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 -Justin Quoting Dmytro Kovalskyy [EMAIL PROTECTED]: Trjorder does not write trajectory file, only nshell.xvg This is true for 3.3.2 and 3.3.1 versions. Dima ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = !DSPAM:47367e03304461801161890! -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org
[gmx-users] g_hbond
Dear all, I have two moleculars in the .trr. I want to use g_hbond to analyze the hydrogen bonds between them. Can g_hbond analyze the hydrogen bonds between two moleculars associated by a H2O molecular? The hydrogen bond may be the following form: -N-HO-HO=C- | H Best regards, 2007-10-17 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Amber to Gromacs
Dear all, I hvae used ANTECHAMBER GAFF of Amber generate a .prmtop and .prmcrd of a small molecular(XK263, a inhibitor of HIV-1 PR). I want to use ffamber99 in Gromacs-3.3.1 to do a simulation of it, but I can't get the force field of the molecular used in Gromacs. On the Homepage of Amber, there is a script to converse the Amber force field to Gromacs. But it can't work without Amber8 or Amber9 installation. I didn't get a Amber8/Amber9 package, can anyone help me to do the conversion? It will be very appreciated! The attached is the .prmtop and the .prmcrd file, another one is the script. They are in a compressed file in the attached. The command used may be: ./amb2gmx.pl --prmtop XK.prmtop --crd XK.prmcrd --outname XK Best regards, 2007-10-13 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = file.rar Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ANTECHAMBER GAFF
Dear gmx-users， I want to use ANTECHAMBER GAFF to generate the topology of a small molecular(HIV-1 Protease inhibitor, Nelfinavir) for gromacs. But It seems to be not so simple. Is there anyone who did the similar thing before? Is there any tutorials? With best regards, 2007-9-29 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: ANTECHAMBER GAFF
Dear gmx-users, With the help of Yang Ye and Mark, I downloaded amb2gmx.pl to transform the topology from AMBER format to GROMACS. But the script requires an AMBER installation to work and I didn't have a AMBER package. How can I go on? Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Gromacs for Aerosol Particle Agglomeration (Lorenzo Isella) 2. Re: Gromacs for Aerosol Particle Agglomeration (Yang Ye) 3. ANTECHAMBER GAFF (Dechang Li) 4. Re: ANTECHAMBER GAFF (Mark Abraham) 5. Re: ANTECHAMBER GAFF (Yang Ye) 6. Re: Reading XTC files from fortran90 (Jones de Andrade) 7. Re: Reading XTC files from fortran90 (Bert de Groot) -- Message: 1 Date: Sat, 29 Sep 2007 15:13:51 +0200 From: Lorenzo Isella [EMAIL PROTECTED] Subject: [gmx-users] Gromacs for Aerosol Particle Agglomeration To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear All, I am 100% new on this list and to Molecular Dynamics in general. This is what I am interested into (and would like to know if Gromacs is then the right tool). I am not really into biology or chemistry, but rather in aerosol science. I am interested in studying how diesel exhaust aerosol particles, generally carried by a turbulent exhaust flow, collide and, by sticking together, give rise to complicated structures (idea of agglomeration). We now leave aside the technicalities (how they stick, what the compenetration depends upon etc.), but first of all I would like to know if Gromacs is the right tool for doing that. Typically, I deal with concentrations around 10^8 particles per cm^3 and I need to follow the evolution of the system for some seconds. The particles carrier-flow is typically turbulent, but collisions are mainly due to Brownian motion (I am thinking about some Langevin dynamics). I have access to a few nodes in a cluster (if that becomes a necessity) but have no experience in running parallel codes. A last (but not least) question: I installed gromacs on my Debian Testing laptop; how do I run the examples/tutorials? Is there any available gromacs code you recommend me to look at for my specific problem or as a good way to learn the ropes? Many thanks Lorenzo -- Message: 2 Date: Sat, 29 Sep 2007 21:54:24 +0800 From: Yang Ye [EMAIL PROTECTED] Subject: Re: [gmx-users] Gromacs for Aerosol Particle Agglomeration To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/29/2007 9:13 PM, Lorenzo Isella wrote: Dear All, I am 100% new on this list and to Molecular Dynamics in general. This is what I am interested into (and would like to know if Gromacs is then the right tool). I am not really into biology or chemistry, but rather in aerosol science. I am interested in studying how diesel exhaust aerosol particles, generally carried by a turbulent exhaust flow, collide and, by sticking together, give rise to complicated structures (idea of agglomeration). We now leave aside the technicalities (how they stick, what the compenetration depends upon etc.), but first of all I would like to know if Gromacs is the right tool for doing that. You may consult the gromacs manual, which is also a good introductory material on the topic of MD. You need to check especially whether the interaction existed in your system can be found in GROMACS' supported inter-particle interaction. Typically, I deal with concentrations around 10^8 particles per cm^3 and I need to follow the evolution of the system for some seconds. The particles carrier-flow is typically turbulent, but collisions are mainly due to Brownian motion (I am thinking about some Langevin dynamics). I have access to a few nodes in a cluster (if that becomes a necessity) but have no experience in running parallel codes. You can leave this question later. A last (but not least) question: I installed gromacs on my Debian Testing laptop; how do I run the examples/tutorials? GROMACS works almost with command-line tools so you need to open the terminal windows to type commands inside them. So get yourself with some basic Linux/Unix commands first if you are no so; then proceed with the tutorial. Is there any available gromacs code you recommend me to look at for my specific problem or as a good way to learn the ropes? Check literature. I guess there would be some MD work done on your topic
[gmx-users] Large VCM problems
Hi, When I used BD or SD simulation, it always occurs a problem called 'Large VCM', but the simulation works well! Is the simulation result believable? Here is my md.mdp file: integrator = bd comm_mode = Angular Tcoupl = berendsen tau_t = 1.0 tc-grps = protein ref_t = 300.0 bd_fric = 6129.788 Is the 'bd_fric' too large? When I used LD simulation,there are the same problems: integrator = sd comm_mode = Angular Tcoupl = berendsen tau_t = 0.2 tc-grps = protein ref_t = 300.0 Thank you for your answers. Dechang Li [EMAIL PROTECTED] 2007-04-16 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Twin-range neighbour searching (NS) with simple NS algorithm not implemented
hi, Can anyone tell me what does this error mean? ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented my md.mdp file was set: ns_type = grid pbc = xyz Thank you very much! Li,DC Department of Engineering Mechanics Tsinghua University Beijing 100084 China Email address: [EMAIL PROTECTED] 2007-01-22 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
