RE: [gmx-users] FES and FE molecule topology
Including Fe2+ should not be very difficult, look at the definitions for Cu2+ or others in ffG53a6.nb or any other forcefield you want to use. You need to find the correct Lennard-Jones parameters C6 and C12 and then validate your model. I am not sure, what the FES molecule is, but developing a topology for molecules is more difficult than for single atoms. Have a look at the Gromacs help section: http://www.gromacs.org/Documentation/How-tos/Parameterization Best wishes Andreas From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of sonali dhindwal [sonali11dhind...@yahoo.co.in] Sent: 05 June 2010 14:31 To: Discussion list for GROMACS users Subject: [gmx-users] FES and FE molecule topology Hello All, Could some one please help me in introducing Fe2+ and FES molecule in protein for simulation studies. But before starting it, I am not able to generate topology file for the same. I have tried to use HICUP database and used CNS topology file. but it is still not working. Please help Thanks and regards -- Sonali Dhindwal -- 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
Re: [gmx-users] Regarding genconf
Hi Vinod, How did you build your top file for input to grompp ? genconf would have given you a multiplied system in .gro structure format. I think you should generate .top file from this .gro file using pdb2gmx and then use that as grompp input. Regards, Nikhil From: jani vinod genomej...@gmail.com To: gmx-users@gromacs.org Sent: Fri, 4 June, 2010 10:54:16 AM Subject: [gmx-users] Regarding genconf Hello, I build a system solvated in water . Then replicated the system using genconf. Now when I am running grompp i am getting following warning Warning: atom name 404 in PH7.top and replicate_systemB.gro does not match (N - C1) Warning: atom name 405 in PH7.top and replicate_systemB.gro does not match (H1 - C2) Warning: atom name 406 in PH7.top and replicate_systemB.gro does not match (H2 - C3) Warning: atom name 407 in PH7.top and replicate_systemB.gro does not match (H3 - N4) Warning: atom name 408 in PH7.top and replicate_systemB.gro does not match (CA - C5) Warning: atom name 409 in PH7.top and replicate_systemB.gro does not match (CB - C6) Warning: atom name 410 in PH7.top and replicate_systemB.gro does not match (CG - O7) Warning: atom name 411 in PH7.top and replicate_systemB.gro does not match (OD1 - P8) Warning: atom name 412 in PH7.top and replicate_systemB.gro does not match (OD2 - O9) Warning: atom name 413 in PH7.top and replicate_systemB.gro does not match (C - O10) Warning: atom name 414 in PH7.top and replicate_systemB.gro does not match (O - O11) Warning: atom name 415 in PH7.top and replicate_systemB.gro does not match (N - C12) Warning: atom name 416 in PH7.top and replicate_systemB.gro does not match (H - C13) Warning: atom name 417 in PH7.top and replicate_systemB.gro does not match (CA - O14) Warning: atom name 418 in PH7.top and replicate_systemB.gro does not match (CB - C15) Warning: atom name 419 in PH7.top and replicate_systemB.gro does not match (C - O16) Warning: atom name 420 in PH7.top and replicate_systemB.gro does not match (O - C17) Warning: atom name 421 in PH7.top and replicate_systemB.gro does not match (N - C18) Warning: atom name 422 in PH7.top and replicate_systemB.gro does not match (H - C19) Warning: atom name 423 in PH7.top and replicate_systemB.gro does not match (CA - C20) and when after ignoring the warning I try to run system my system get distorted. Thanks vinod -- 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
Re: [gmx-users] Regarding genconf
Thanks for reply ,The problem is solved .The problem was with topology file . On Fri, Jun 4, 2010 at 4:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: jani vinod wrote: Hello, I build a system solvated in water . Then replicated the system using genconf. Now when I am running grompp i am getting following warning Warning: atom name 404 in PH7.top and replicate_systemB.gro does not match (N - C1) Warning: atom name 405 in PH7.top and replicate_systemB.gro does not match (H1 - C2) Warning: atom name 406 in PH7.top and replicate_systemB.gro does not match (H2 - C3) Warning: atom name 407 in PH7.top and replicate_systemB.gro does not match (H3 - N4) Warning: atom name 408 in PH7.top and replicate_systemB.gro does not match (CA - C5) Warning: atom name 409 in PH7.top and replicate_systemB.gro does not match (CB - C6) Warning: atom name 410 in PH7.top and replicate_systemB.gro does not match (CG - O7) Warning: atom name 411 in PH7.top and replicate_systemB.gro does not match (OD1 - P8) Warning: atom name 412 in PH7.top and replicate_systemB.gro does not match (OD2 - O9) Warning: atom name 413 in PH7.top and replicate_systemB.gro does not match (C - O10) Warning: atom name 414 in PH7.top and replicate_systemB.gro does not match (O - O11) Warning: atom name 415 in PH7.top and replicate_systemB.gro does not match (N - C12) Warning: atom name 416 in PH7.top and replicate_systemB.gro does not match (H - C13) Warning: atom name 417 in PH7.top and replicate_systemB.gro does not match (CA - O14) Warning: atom name 418 in PH7.top and replicate_systemB.gro does not match (CB - C15) Warning: atom name 419 in PH7.top and replicate_systemB.gro does not match (C - O16) Warning: atom name 420 in PH7.top and replicate_systemB.gro does not match (O - C17) Warning: atom name 421 in PH7.top and replicate_systemB.gro does not match (N - C18) Warning: atom name 422 in PH7.top and replicate_systemB.gro does not match (H - C19) Warning: atom name 423 in PH7.top and replicate_systemB.gro does not match (CA - C20) and when after ignoring the warning I try to run system my system get distorted. Whenever grompp throws warnings like this, don't ignore them and plow ahead, it's a recipe for disaster. The [molecules] section of your topology is out of order with respect to your coordinate file, so parameters for different species are being applied incorrectly. -Justin Thanks vinod -- 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/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 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] which flag for the force
Hi all, I want to get the forces out of the .trr file using the template.c given. My question is what flag should I use in the last loop to get the force f? I don't find anything in the directory which is given in the example. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)
Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used pull_geometry = direction. However, at the end of the simulation, I notice that the desired alignment (with z) was not maintained. The molecule is pulled away from z and eventually crosses the PBC. I took a good look at gmx-list and noticed that you rode conducting tests with this option. Could you give me a light on this problem too? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Constraint causing system to explode (Warren Gallin) 2. PMF in vacuum (chris.ne...@utoronto.ca) 3. Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman) 4. vibrational spectra of glucose (Nilesh Dhumal) -- Message: 2 Date: Thu, 27 May 2010 12:12:03 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum To: gmx-users@gromacs.org Message-ID: 20100527121203.orb2sq228s4ow...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. 6. regarding histo.png: can you confirm that the few very short gaussians are due to less sampling in a few windows? In any event, the overlap looks good. Chris -- original message -- Hello Chris, thanks for your attention. I'm sending you some links to some tests I performed. As I said you will notice that depending on the parameter used my simulation shows PMF profiles quite different. Especially what concerns to the difference between the use or not of the PBC. https://sites.google.com/site/fileti/files/test1.jpg https://sites.google.com/site/fileti/files/test2.jpg https://sites.google.com/site/fileti/files/histo.png I have constructed two very similar topologies (ben-a.itp and ben-b.itp) where I put a virtual site in the center of benzene. This sites were restrained to keep my molecules fixed distance desired. The basic details of the simulations are given below:1000 define = -DPOSRES integrator = sd tinit= 0 dt = 0.002 nsteps = 500 or 50 comm-mode= angular nstcomm = 1 comm-grps= System bd-fric = 1 ld-seed = 1993 nstlist = 5 ns_type = simple pbc = no or xyz periodic_molecules = no rlist= 0 coulombtype = Cut-off vdw-type = Cut-off rvdw = 0 DispCorr = no
[gmx-users] tutorial of free energy calculations
Dear GMX users, I don't know why I can't open the tutorial of free energy calculations on this website http://www.gromacs.org/Documentation/Tutorials. Can you open it? Thanks very much! All the best, fancy-- 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
Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization
I agree the code is fine. Is there a parameter that I need to change to increase the tolerance? I have issues energy minimizing a small molecule in the presence of a macromolecule. One work around is to increase the energy of the small molecule, so that the macromolecule no longer dominates the energetics. I would appreciate your input. Art On Jun 4, 2010, at 5:45 PM, Mark Abraham wrote: - Original Message - From: Arthur Roberts aroberts99...@yahoo.com Date: Saturday, June 5, 2010 4:57 Subject: [gmx-users] How to increase the tolerance for conjugate gradient minimization To: gmx users gmx-users@gromacs.org Hi, all, Is there a way to increase the tolerance for Conjugate Gradient energy minimization? It seems that I can only get a Tolerance (Fmax) = 1e-4 emtol doesn't seem to do the trick. I tried several values. The code's fine in 4.0.7. Does your .mdp value match that reported in the .log file? Ditto in gmxcheck on the .tpr? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 Art Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- 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] NPT system density
Hello, I have 125 hexane molecules in a box of 0.25nm3. The desnity I calculate from this number of molecules is approx. 71000 Kg/m3. To make sure that the density remains constant I am doing NPT simulation. From this simulation I see the density is 577 Kg/m3. and the volume is 30 nm3. Please guide me why is this...also how can I get the compressibility for my system? *Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449 Density (SI)577.9146.978043.802522.02643 20.2684* Thanks, Statistics over 5001 steps [ 0. thru 10. ps ], 21 data sets The term 'Cons. rmsd ()' is averaged over 501 frames All other averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Angle 4390.56265.163204.66358.3917 584.034 Ryckaert-Bell. 986.833112.50383.376726.1601 261.653 LJ-14 649.58130.911628.86853.82766 38.2843 Coulomb-14 -289.755 25.8719.19928 8.3746 83.7628 LJ (SR)-3367.8562.512655.3718 -10.0486 -100.506 Coulomb (SR)675.83921.15437.92426 -6.79315 -67.9451 Coul. recip. 927.3222.68437.25885-7.4434 -74.4489 Potential 3972.53379.824316.992 72.469 724.835 Kinetic En. 6331.94257.353 242.7929.5579 295.639 Total Energy10304.5567.222484.728102.027 1020.47 Temperature 297.366 12.08611.40211.38812 13.884 Pressure (bar) -30.0299746.524745.665 -12.3992 -124.017 Cons. rmsd ()3.73576e-06 2.80181e-07 2.35022e-07 5.28277e-08 5.28383e-07 Box-X 4.98423 0.0200728 0.0109722 -0.00582152 -0.0582268 Box-Y 2.49212 0.0100364 0.0054861 -0.00291076 -0.0291134 *Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449 Density (SI)577.9146.978043.802522.02643 20.2684* pV -55.98791393.391391.81 -22.9985 -230.031 #Surf*SurfTen218.214871.454871.37 -9.30662 -93.0848 T-HEX 297.366 12.08611.40211.38812 13.884 Lamb-HEX1.00011 0.000588089 0.000561362 -6.07045e-05 -0.000607166 Heat Capacity Cv: 12.5027 J/mol K (factor = 0.0016519) Isothermal Compressibility: 0.00011012 /bar Adiabatic bulk modulus:9080.99 bar mdp file: title = Hexane cpp = /lib/cpp ;Run control integrator = md dt = 0.002; ps ! nsteps = 5000; total 1.0 ps. nstcomm = 1; frequency for center of mass motion removal ;Output control nstenergy = 10; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 10; frequency to write coordinates/velocity/force to output trajectory file nstvout = 0 nstfout = 10 nstlog = 10; frequency to write energies to log file nstxtcout = 10 ;Neighbor searching nstlist = 10; neighborlist will be updated at least every 10 steps ;ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= cut-off ;Cut-offs rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ;Temperature couplingBerendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = HEX ;sol tau_t = 0.1 ;0.1 ref_t = 300 ;300 ;Pressure coupling: Pressure coupling is not on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ;Velocity generationGenerate velocites is on at 300 K. Manual p155 gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs pbc=xyz -- 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] PBC
Morteza Khabiri wrote: Dear users I have a dimer protein in the water box. It was run for 30ns. during the simulation dimer split to two monomer. This things happen bc of PBC. ( I checked it by vmd pbc option ) to have a two monomer together during trajectories (for visualization) I have used the following command: trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol but it is not working. Is there any other method or command which I could implement pbc in trajectory. Thanks in advance Morteza Shahab Shariati wrote: You can use other flags of trjconv command as follows: Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center -- 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] implementing a pulsed, time-dependent electric field in gromacs
Dear all: After I read the paper, Picosecond Melting of Ice by an Infrared Laser Pulse: A Simulation Study (Carl Caleman and David van der Spoel, Angew. Chem. Int. Ed., 2008, 47, 1417-1420), I decided to implement a time-dependent electric field on my simulation system. But when I read the gromacs manual I found it hasn't been implemented in gromacs yet. So may I ask is it possible to apply a pulsed, time-dependent electric field in the newest version of gromacs? Thank you! Fangyong -- 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
Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization
Hi Arthur, The most useful option from my experience is to run Gromacs in double precision. You also can try to make emstep smaller (after an initial minimisation of the crude structure) and use l-bfgs. Good luck, Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- Arthur Roberts wrote: I agree the code is fine. Is there a parameter that I need to change to increase the tolerance? I have issues energy minimizing a small molecule in the presence of a macromolecule. One work around is to increase the energy of the small molecule, so that the macromolecule no longer dominates the energetics. I would appreciate your input. Art On Jun 4, 2010, at 5:45 PM, Mark Abraham wrote: - Original Message - From: Arthur Roberts aroberts99...@yahoo.com Date: Saturday, June 5, 2010 4:57 Subject: [gmx-users] How to increase the tolerance for conjugate gradient minimization To: gmx users gmx-users@gromacs.org Hi, all, Is there a way to increase the tolerance for Conjugate Gradient energy minimization? It seems that I can only get a Tolerance (Fmax) = 1e-4 emtol doesn't seem to do the trick. I tried several values. The code's fine in 4.0.7. Does your .mdp value match that reported in the .log file? Ditto in gmxcheck on the .tpr? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 Art Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- 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
Re: [gmx-users] which flag for the force
- Original Message - From: Sebastian Waltz sebastian.wa...@physik.uni-freiburg.de Date: Tuesday, June 8, 2010 18:48 Subject: [gmx-users] which flag for the force To: gmx-users@gromacs.org Hi all, I want to get the forces out of the .trr file using the template.c given. My question is what flag should I use in the last loop to get the force f? I don't find anything in the directory which is given in the example. Look at how (e.g.) trjconv does it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] add external force
Hi, I would like to add an external force f(x) on some atoms during the simulation, where x is the Cartesian coordinates of these atoms. Each component of the force can only be calculated with the whole set of coordinates, i.e., (f1, f2, ..., fn) = f(x1, x2, ..., xn) Is there a possible way to do it with Gromacs simply? Thank you! Ting -- 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
Re: [gmx-users] add external force
- Original Message - From: Ting Zhou coomt...@gmail.com Date: Tuesday, June 8, 2010 19:13 Subject: [gmx-users] add external force To: gmx-users@gromacs.org Hi, I would like to add an external force f(x) on some atoms during the simulation, where x is the Cartesian coordinates of these atoms. Each component of the force can only be calculated with the whole set of coordinates, i.e., (f1, f2, ..., fn) = f(x1, x2, ..., xn) If you potentially need to know every coordinate to calculate each force, then you will have to either run in serial, or emulate the behaviour in write_trxframe to gather the coordinates and scatter the forces at useful time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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
Re: [gmx-users] add external force
On 06/08/2010 11:18 AM, Mark Abraham wrote: - Original Message - From: Ting Zhou coomt...@gmail.com Date: Tuesday, June 8, 2010 19:13 Subject: [gmx-users] add external force To: gmx-users@gromacs.org Hi, I would like to add an external force f(x) on some atoms during the simulation, where x is the Cartesian coordinates of these atoms. Each component of the force can only be calculated with the whole set of coordinates, i.e., (f1, f2, ..., fn) = f(x1, x2, ..., xn) If you potentially need to know every coordinate to calculate each force, then you will have to either run in serial, or emulate the behaviour in write_trxframe to gather the coordinates and scatter the forces at useful time. Mark Are you talking about modifying the source? Is there a lagged script interface to calculate forces? Best, Ting -- 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] helical parameters for DNA
Hi gromacs users I want to simulate pr-dna by gromacs.I read a article (Biophysical Journal 87(6) 3799–3813) inwhich helical parameters for DNA (rise, slide, twist, roll, tilt, shift) calculated by md simulation, but I did not understand two things: How and what command these parameters were calculated? I read gromacs manual. in that there is only g helix and g helixorient for Protein specific analysis. can any body help me how to do this ? -- 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
Re: [gmx-users] NPT system density
Hi, For one thing; to keep density constant (as in fixed) you want NVT, not NPT. NPT could, depending on your starting state, allow for initial drift in the system size. Cheers, Erik Marklund Moeed skrev: Hello, I have 125 hexane molecules in a box of 0.25nm3. The desnity I calculate from this number of molecules is approx. 71000 Kg/m3. To make sure that the density remains constant I am doing NPT simulation. From this simulation I see the density is 577 Kg/m3. and the volume is 30 nm3. Please guide me why is this...also how can I get the compressibility for my system? *Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449 Density (SI)577.9146.978043.80252 2.0264320.2684* Thanks, Statistics over 5001 steps [ 0. thru 10. ps ], 21 data sets The term 'Cons. rmsd ()' is averaged over 501 frames All other averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Angle 4390.56265.163204.663 58.3917584.034 Ryckaert-Bell. 986.833112.50383.3767 26.1601261.653 LJ-14 649.58130.911628.8685 3.8276638.2843 Coulomb-14 -289.755 25.8719.19928 8.374683.7628 LJ (SR)-3367.8562.512655.3718 -10.0486 -100.506 Coulomb (SR)675.83921.15437.92426 -6.79315 -67.9451 Coul. recip. 927.3222.68437.25885-7.4434 -74.4489 Potential 3972.53379.824316.992 72.469724.835 Kinetic En. 6331.94257.353 242.79 29.5579295.639 Total Energy10304.5567.222484.728 102.0271020.47 Temperature 297.366 12.08611.4021 1.38812 13.884 Pressure (bar) -30.0299746.524745.665 -12.3992 -124.017 Cons. rmsd ()3.73576e-06 2.80181e-07 2.35022e-07 5.28277e-08 5.28383e-07 Box-X 4.98423 0.0200728 0.0109722 -0.00582152 -0.0582268 Box-Y 2.49212 0.0100364 0.0054861 -0.00291076 -0.0291134 *Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449 Density (SI)577.9146.978043.80252 2.0264320.2684* pV -55.98791393.391391.81 -22.9985 -230.031 #Surf*SurfTen218.214871.454871.37 -9.30662 -93.0848 T-HEX 297.366 12.08611.4021 1.38812 13.884 Lamb-HEX1.00011 0.000588089 0.000561362 -6.07045e-05 -0.000607166 Heat Capacity Cv: 12.5027 J/mol K (factor = 0.0016519) Isothermal Compressibility: 0.00011012 /bar Adiabatic bulk modulus:9080.99 bar mdp file: title = Hexane cpp = /lib/cpp ;Run control integrator = md dt = 0.002; ps ! nsteps = 5000; total 1.0 ps. nstcomm = 1; frequency for center of mass motion removal ;Output control nstenergy = 10; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 10; frequency to write coordinates/velocity/force to output trajectory file nstvout = 0 nstfout = 10 nstlog = 10; frequency to write energies to log file nstxtcout = 10 ;Neighbor searching nstlist = 10; neighborlist will be updated at least every 10 steps ;ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= cut-off ;Cut-offs rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ;Temperature couplingBerendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = HEX ;sol tau_t = 0.1 ;0.1 ref_t = 300 ;300 ;Pressure coupling: Pressure coupling is not on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ;Velocity generationGenerate velocites is on at 300 K. Manual p155 gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs pbc=xyz -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se
Re: [gmx-users] helical parameters for DNA
shahab shariati wrote: Hi gromacs users I want to simulate pr-dna by gromacs.I read a article (Biophysical Journal 87(6) 3799–3813) inwhich helical parameters for DNA (rise, slide, twist, roll, tilt, shift) calculated by md simulation, but I did not understand two things: How and what command these parameters were calculated? There's nothing in Gromacs that will do all that by default. I read gromacs manual. in that there is only g helix and g helixorient for Protein specific analysis. can any body help me how to do this ? You'll probably have to code it yourself. These are all simple geometric parameters, so it shouldn't be that difficult. -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/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] PMF in vacuum and pull direction
Dear Eudes: You can make my job a whole lot easier! First, please go back through all of the comments that I gave you last time and reply to them one by one. Did you do them? What did you see? Second, please include your new .mdp and some quantitative results to better explain what you see (e.g. your .px file and a description of why the values are not what you expect). Sorry if this sounds annoying, but there's no point in my working in the dark. Chris. -- original message -- Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used pull_geometry = direction. However, at the end of the simulation, I notice that the desired alignment (with z) was not maintained. The molecule is pulled away from z and eventually crosses the PBC. I took a good look at gmx-list and noticed that you rode conducting tests with this option. Could you give me a light on this problem too? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br [Hide Quoted Text] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Constraint causing system to explode (Warren Gallin) 2. PMF in vacuum (chris.ne...@utoronto.ca) 3. Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman) 4. vibrational spectra of glucose (Nilesh Dhumal) -- Message: 2 Date: Thu, 27 May 2010 12:12:03 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum To: gmx-users@gromacs.org Message-ID: 20100527121203.orb2sq228s4ow...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. 6. regarding histo.png: can you confirm that the few very short gaussians are due to less sampling in a few windows? In any event, the overlap looks good. Chris -- original message -- Hello Chris, thanks for your attention. I'm sending you some links to some tests I performed. As I said you will notice that depending on the parameter used my simulation shows PMF profiles quite different. Especially what concerns to the difference between the use or not of the PBC. https://sites.google.com/site/fileti/files/test1.jpg https://sites.google.com/site/fileti/files/test2.jpg https://sites.google.com/site/fileti/files/histo.png I have constructed two very similar topologies (ben-a.itp and ben-b.itp) where I put a virtual site in the center of benzene. This sites were restrained to keep my molecules fixed distance desired. The basic details of the simulations are given below:1000 define = -DPOSRES integrator = sd tinit= 0 dt = 0.002 nsteps = 500 or 50 comm-mode
[gmx-users] thermodynamic integration yields different values in gromacs 3.3.1 and later versions
Dear Gromacs users, I am doing thermodynamic integration in order to compute the change in free energy upon increasing the electric charges of a water molecule from zero (lambda=0) to its actual partial charges (lambda=1). I get significantly different results of dVpot/dlambda with Gromacs 3.3.1 on one hand and 3.3.3 (and later versions) on the other hand. I use linear scaling of the charges with lambda. There is a difference for all lambda values but it's most prominent near lambda=0, where the values are different by an order of magnitude. The difference is independent of the trajectory, i.e., when I use the trajectory generated with 3.3.1 and rerun it with 3.3.3, I get the same results as if I had generated the trajectory with 3.3.3 directly. Is this a known phenomenon? Can anyone tell me what is the difference between versions 3.3.1 and later versions in this context? Are there any hidden corrections that have been added between 3.3.1 and 3.3.3? Thanks Emanuel -- 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: helical parameters for DNA
Hello, you can use for example Curves (Nucleic Acids Research, 2009, Vol. 37, No. 17 5917-5929) or 3DNA (http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html) to calculate them from any trajectory, I did but never used gromacs for this, I don't know if it is possible. Hope this helps, Best Attilio 2010/6/8 shahab shariati shahab.shari...@gmail.com Hi gromacs users I want to simulate pr-dna by gromacs.I read a article (Biophysical Journal 87(6) 37993813) inwhich helical parameters for DNA (rise, slide, twist, roll, tilt, shift) calculated by md simulation, but I did not understand two things: How and what command these parameters were calculated? I read gromacs manual. in that there is only g helix and g helixorient for Protein specific analysis. can any body help me how to do this ? -- 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 ¤¤¤ Attilio Vittorio Vargiu, PhD SLACS Department of Physics, University of Cagliari Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700 09042 Monserrato (CA), Italy e-mail1: var...@dsf.unica.it e-mail2: attilio.var...@gmail.com Phone: +390706754847 Fax: +39070510171 ¤¤¤ SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.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/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
Re: [gmx-users] thermodynamic integration yields different values in gromacs 3.3.1 and later versions
schn...@uni-heidelberg.de wrote: Dear Gromacs users, I am doing thermodynamic integration in order to compute the change in free energy upon increasing the electric charges of a water molecule from zero (lambda=0) to its actual partial charges (lambda=1). I get significantly different results of dVpot/dlambda with Gromacs 3.3.1 on one hand and 3.3.3 (and later versions) on the other hand. I use linear scaling of the charges with lambda. There is a difference for all lambda values but it's most prominent near lambda=0, where the values are different by an order of magnitude. The difference is independent of the trajectory, i.e., when I use the trajectory generated with 3.3.1 and rerun it with 3.3.3, I get the same results as if I had generated the trajectory with 3.3.3 directly. Is this a known phenomenon? Can anyone tell me what is the difference between versions 3.3.1 and later versions in this context? Are there any hidden corrections that have been added between 3.3.1 and 3.3.3? Are you using PME? There is a bug in the 3.3.1 free energy code with PME. It is a known issue, but unfortunately it looks like the mailing list search is down so I can't locate the thread where this is discussed. -Justin Thanks Emanuel -- 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/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
Re: [gmx-users] add external force
- Original Message - From: Ting Zhou coomt...@gmail.com Date: Tuesday, June 8, 2010 19:26 Subject: Re: [gmx-users] add external force To: Discussion list for GROMACS users gmx-users@gromacs.org On 06/08/2010 11:18 AM, Mark Abraham wrote: - Original Message - From: Ting Zhou coomt...@gmail.com Date: Tuesday, June 8, 2010 19:13 Subject: [gmx-users] add external force To: gmx-users@gromacs.org Hi, I would like to add an external force f(x) on some atoms during the simulation, where x is the Cartesian coordinates of these atoms. Each component of the force can only be calculated with the whole set of coordinates, i.e., (f1, f2, ..., fn) = f(x1, x2, ..., xn) If you potentially need to know every coordinate to calculate each force, then you will have to either run in serial, or emulate the behaviour in write_trxframe to gather the coordinates and scatter the forces at useful time. Mark Are you talking about modifying the source? Yes. Perhaps TINKER or something is more amenable to the kind of computational experiment that it sounds like you might be doing. Is there a lagged script interface to calculate forces? I don't know what this is, but no. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Simulation with CsCl
Hi all: I am trying to simulate a polysaccharide in solution of water and CsCl, but cesium is not parametrized in the gromacs 4. I am using the force field GROMOS 96. I have looked for the parameters of Cs+ in the OPLS Force field and I have created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include the parameters for Cs+ in the ions.itp file, but it didn't work, Can someone help me? Thanks in advance. Cecilia. -- 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
Re: [gmx-users] Simulation with CsCl
Cecilia Fernándz Gauna wrote: Hi all: I am trying to simulate a polysaccharide in solution of water and CsCl, but cesium is not parametrized in the gromacs 4. I am using the force field GROMOS 96. I have looked for the parameters of Cs+ in the OPLS Force field and I have created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include the parameters for Cs+ in the ions.itp file, but it didn't work, Can someone help me? Not unless you define what didn't work means. What did you try? What was the error message? What tool gave you a problem? Also, you start by saying you're trying to use Gromos96, but then mention OPLS parameters. I hope you're not trying to mix and match force fields... http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Thanks in advance. Cecilia. -- 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/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] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)
Dear Chris, I'm so sorry for surperficial email. You are correct because in the previous message I forgot to mention that now the simulation was performed in water (naturally with PBC). The main parameters of the simulation are given below. As I said, I wish to keep the displacement of the pulled molecule at the z-axis, but I'm not getting with this protocol. For the vacuum I followed the tips you gave me earlier and had success! Thanks eef title = Umbrella pulling simulation integrator = sd dt = 0.002 nsteps = 300 constraint_algorithm = lincs constraints = all-bonds nstlist = 5 ns_type = simple rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = Cut-off Tcoupl = V-rescale tc_grps = system tau_t = 0.1 ref_t = 298 Pcoupl = no pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 pbc = xyz ; Pull code pull = umbrella pull_geometry = direction pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = BEN1 pull_group1 = BEN2 pull_vec1 = 0 0 1 pull_rate1 = 0.001 pull_k1 = 1600 Message: 4 Date: Tue, 08 Jun 2010 08:05:23 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum and pull direction To: gmx-users@gromacs.org Message-ID: 20100608080523.i6oo62he1wwc0...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: You can make my job a whole lot easier! First, please go back through all of the comments that I gave you last time and reply to them one by one. Did you do them? What did you see? Second, please include your new .mdp and some quantitative results to better explain what you see (e.g. your .px file and a description of why the values are not what you expect). Sorry if this sounds annoying, but there's no point in my working in the dark. Chris. -- original message -- Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used pull_geometry = direction. However, at the end of the simulation, I notice that the desired alignment (with z) was not maintained. The molecule is pulled away from z and eventually crosses the PBC. I took a good look at gmx-list and noticed that you rode conducting tests with this option. Could you give me a light on this problem too? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br Message: 2 Date: Thu, 27 May 2010 12:12:03 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum To: gmx-users@gromacs.org Message-ID: 20100527121203.orb2sq228s4ow...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. 6. regarding histo.png: can you confirm that the few very short
[gmx-users] 100 step md run: Infinite giga flopses error
Hi, I am running a very short md run for 100 steps and I get the Infinite giga flopses error. I stored info at every step to check if the simulation is running. And the log file has all the variables for each time-step with reasonable values. I don't understand the meaning of the message at the end of the log file. nodetime = 0! Infinite Giga flopses! Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 This is not the first time I have encountered this problem with short md runs. Parameter file ; VARIOUS PREPROCESSING OPTIONS title=NPT simulation for a 2D WCA system cpp =/lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.0001 nsteps = 100 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1 ; Write every nth step to the log nstenergy= 0 ; Write energies at every n step nstxtcout= 0 ; Do not write a compressed tr ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Cut-off rcoulomb = 1.1225 vdw-type = Cut-off rvdw = 1.1225 ; Temperature coupling tcoupl = v-rescale tc-grps = AR tau_t= 0.1 ref_t= 0.1 ld_seed =-1 ; Pressure coupling pcoupl = Berendsen pcoupltype = semiisotropic tau-p= 0.1 0.1 compressibility = 1e-5 0 ;Dont know ref-p= 58 0 ;Generate velocities for startup run gen_vel =yes gen_temp =1 gen_seed =-1 ;Non equilibrium MD steps freezegrps =AR freezedim =N N Y Error: At the end of log file nodetime = 0! Infinite Giga flopses! Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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
Re: [gmx-users] 100 step md run: Infinite giga flopses error
Sai Pooja wrote: Hi, I am running a very short md run for 100 steps and I get the Infinite giga flopses error. I stored info at every step to check if the simulation is running. And the log file has all the variables for each time-step with reasonable values. I don't understand the meaning of the message at the end of the log file. nodetime = 0! Infinite Giga flopses! Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 This is not the first time I have encountered this problem with short md runs. This isn't really a problem, per se. Gromacs is fast. If you look at the benchmarks in the Gromacs 4 paper, you can get several hundred steps of MD per second for a relatively small system. So essentially your run probably finished in less than a second, and mdrun recorded that as zero time. Division by zero = infinite performance :) If you think there's something else actually wrong, please at least provide a description of how large your system is, how long the run actually took to complete, if you're running in parallel, etc. -Justin Parameter file ; VARIOUS PREPROCESSING OPTIONS title=NPT simulation for a 2D WCA system cpp =/lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.0001 nsteps = 100 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1 ; Write every nth step to the log nstenergy= 0 ; Write energies at every n step nstxtcout= 0 ; Do not write a compressed tr ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Cut-off rcoulomb = 1.1225 vdw-type = Cut-off rvdw = 1.1225 ; Temperature coupling tcoupl = v-rescale tc-grps = AR tau_t= 0.1 ref_t= 0.1 ld_seed =-1 ; Pressure coupling pcoupl = Berendsen pcoupltype = semiisotropic tau-p= 0.1 0.1 compressibility = 1e-5 0 ;Dont know ref-p= 58 0 ;Generate velocities for startup run gen_vel =yes gen_temp =1 gen_seed =-1 ;Non equilibrium MD steps freezegrps =AR freezedim =N N Y Error: At the end of log file nodetime = 0! Infinite Giga flopses! Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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/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: Simulation with CsCl
Hi all: I am trying to simulate a polysaccharide in solution of water and CsCl, but cesium is not parametrized in the gromacs 4. I am using the force field GROMOS 96. I have looked for the parameters of Cs+ in the OPLS Force field and I have created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include the parameters for Cs+ in the ions.itp file, but it didn't work, Can someone help me? Thanks in advance. Cecilia. Cecilia - You do not need so many files so cesium. Just copy your parameters to the force field used and create the topology entry for cesium similar to [ moleculetype ] Ar 1 [ atoms ] 1 Ar1Ar Ar0 0.0 Do not forget, cesium+ is an ion... -- Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] gromacs (git) with charmm FF lipid freezing problem
Hello, I am trying to simulate a DPPC bilayer, 180 lipids total, ~13000 TIP3 and 50 K, 50 Cl counter-ions. The standard charmm27r DPPC parameters have very large charge groups, so I went through them and made them smaller (4 atoms each, on average), following the comments from grompp. I have tried the C27 parameters, recent parameters by Sonne, et al. (Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension. Jacob Sonne, et al. Biophysical Journal, 15 June 2007. Vol. 92, Issue 12, pp. 4157-4167) as well as the latest Charmm36 parameters available from Alex MacKerrell's website. The last two do not require surface tension so I was using semiisotropic pressure coupling with the same compressibility for XY and Z (4.5e-5). For charmm27 parameters I set XY compressibility to 0 (constant area). I am using all-bond constraints with LINCS and the CHARMM_TIP3P water model. I have tried langevin dynamics as well as the standard md integrator. The temperature is coupled separately for DPPC and non-DPPC at 323.15K. When I run any simulation for 10 ns, I get what looks like frozen lipids. They become very straight and aligned with each other, sometimes intercalated. I'm not sure why this is happening... It may be that the lipids are using incorrect dihedral and/or angle parameters (only charges are set explicitly in my DPPC ITP files, everything else is in the base ffnb.itp) Any guesses as to why this may be happening? Anything specific I should be analyzing? I see a steady decrease in LR coulombic potential which seems to change depending on my fourierspacing... so I wonder if my PME settings are wrong. Here is part my MDP: integrator = sd define = -DCHARMM_TIP3P nsteps = 5 dt = 0.002 bd-fric = 0 ld-seed = -1 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 1000 xtc-precision = 1000 nstcomm = 5 nstcalcenergy = 5 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rcoulomb = 1.3 pme_order = 6 ewald_rtol = 1e-5 vdwtype = Switch rvdw= 1.3 rvdw_switch = 1.0 rlist = 1.3 rlistlong = 1.5 fourierspacing = 0.12 tc-grps = DPPC non-DPPC tau_t= 1 1 ref_t = 323.15 323.15 pcoupl = Berendsen pcoupltype = semiisotropic tau_p= 1.0 ref_p= 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = yes gen_temp = 323 gen_seed = -1 constraints = all-bonds constraint-algorithm = Lincs lincs-iter = 1 lincs-order = 6 lincs-warnangle = 60 morse= no -- 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] printing coordinates using template.c
Hello gmx users !! I was trying to use template.c. There I printed out the coordinates of a trajectory file using the printf statement as under: printf(Coordinates at t=%8.3f : %8.5f %8.5f %8.5f\n,fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]); The output was Reading frame 100 time 4400.000 Coordinates at t=4400.000 : 9.34053 4.26640 8.23887 This is the output of the 4400.000 th time or 100th frame of the first Atom in the trr file. Secondly, I dumped the 100th frame using tpbconv (of the same trajectory as above) as: trjconv -s *.tpr -f *.trr -dump 4400.00 -o frame100.pdb The frame100.pdb reads as: ATOM 1 N NGL A 1 93.405 42.664 82.389 1.00 0.00 ATOM 2 H1 NGL A 1 93.849 42.216 81.599 1.00 0.00 ATOM 3 H2 NGL A 1 93.914 43.464 82.737 1.00 0.00 ATOM 4 H3 NGL A 1 93.577 41.958 83.090 1.00 0.00 ATOM 5 CA NGL A 1 91.980 42.980 82.205 1.00 0.00 ATOM 6 HA NGL A 1 91.538 41.996 82.050 1.00 0.00 ATOM 7 CB NGL A 1 91.260 43.708 83.336 1.00 0.00 ATOM 8 HB1 NGL A 1 90.206 43.782 83.068 1.00 0.00 ATOM 9 HB2 NGL A 1 91.603 44.742 83.372 1.00 0.00 We can clearly see the difference in the coordinates of the 1st Atom (ATOM 1 N). That is the coordinates produced by the template are different than those of trjconv's. Can someone help me out to correctly printf the x, y z coordinate using the template.c file. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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
Re: [gmx-users] printing coordinates using template.c
Chandan Choudhury wrote: Hello gmx users !! I was trying to use template.c. There I printed out the coordinates of a trajectory file using the printf statement as under: printf(Coordinates at t=%8.3f : %8.5f %8.5f %8.5f\n,fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]); The output was Reading frame 100 time 4400.000 Coordinates at t=4400.000 : 9.34053 4.26640 8.23887 This is the output of the 4400.000 th time or 100th frame of the first Atom in the trr file. Secondly, I dumped the 100th frame using tpbconv (of the same trajectory as above) as: trjconv -s *.tpr -f *.trr -dump 4400.00 -o frame100.pdb The frame100.pdb reads as: ATOM 1 N NGL A 1 93.405 42.664 82.389 1.00 0.00 ATOM 2 H1 NGL A 1 93.849 42.216 81.599 1.00 0.00 ATOM 3 H2 NGL A 1 93.914 43.464 82.737 1.00 0.00 ATOM 4 H3 NGL A 1 93.577 41.958 83.090 1.00 0.00 ATOM 5 CA NGL A 1 91.980 42.980 82.205 1.00 0.00 ATOM 6 HA NGL A 1 91.538 41.996 82.050 1.00 0.00 ATOM 7 CB NGL A 1 91.260 43.708 83.336 1.00 0.00 ATOM 8 HB1 NGL A 1 90.206 43.782 83.068 1.00 0.00 ATOM 9 HB2 NGL A 1 91.603 44.742 83.372 1.00 0.00 We can clearly see the difference in the coordinates of the 1st Atom (ATOM 1 N). That is the coordinates produced by the template are different than those of trjconv's. Can someone help me out to correctly printf the x, y z coordinate using the template.c file. Both are correct. Gromacs tools use nm units, and PDB files use Angstrom. -Justin Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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/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: printing coordinates using template.c
Chandan - Hmm... What's the problem? template.c gives the numbers in NANOMETERS while PDB file contains them in ANGSTROMS. To my knowledge, nowadays gromacs people use XDRFILE library to work with trajectories - http://www.gromacs.org/index.php?title=Download_%26_Installation -- Dr. Vitaly Chaban Hello gmx users !! I was trying to use template.c. There I printed out the coordinates of a trajectory file using the printf statement as under: printf(Coordinates at t=%8.3f : %8.5f %8.5f %8.5f\n,fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]); The output was Reading frame 100 time 4400.000 Coordinates at t=4400.000 : 9.34053 4.26640 8.23887e This is the output of the 4400.000 th time or 100th frame of the first Atom in the trr file. Secondly, I dumped the 100th frame using tpbconv (of the same trajectory as above) as: trjconv -s *.tpr -f *.trr -dump 4400.00 -o frame100.pdb The frame100.pdb reads as: ATOM 1 N NGL A 1 93.405 42.664 82.389 1.00 0.00 ATOM 2 H1 NGL A 1 93.849 42.216 81.599 1.00 0.00 ATOM 3 H2 NGL A 1 93.914 43.464 82.737 1.00 0.00 ATOM 4 H3 NGL A 1 93.577 41.958 83.090 1.00 0.00 ATOM 5 CA NGL A 1 91.980 42.980 82.205 1.00 0.00 ATOM 6 HA NGL A 1 91.538 41.996 82.050 1.00 0.00 ATOM 7 CB NGL A 1 91.260 43.708 83.336 1.00 0.00 ATOM 8 HB1 NGL A 1 90.206 43.782 83.068 1.00 0.00 ATOM 9 HB2 NGL A 1 91.603 44.742 83.372 1.00 0.00 We can clearly see the difference in the coordinates of the 1st Atom (ATOM 1 N). That is the coordinates produced by the template are different than those of trjconv's. Can someone help me out to correctly printf the x, y z coordinate using the template.c file. Thanks Chandan -- 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
RE: [gmx-users] PME problem on BG/P cluster
Dear Mark, When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any problem. So I guess it's related to the assembly loops for BG. Thanks, Lanyuan From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Date: Sat, 5 Jun 2010 03:31:33 +1000 Subject: Re: [gmx-users] PME problem on BG/P cluster - Original Message - From: LuLanyuan lulany...@msn.com Date: Saturday, June 5, 2010 2:01 Subject: [gmx-users] PME problem on BG/P cluster To: gmx-users@gromacs.org Hello, I got a weird problem by running Gromacs 4.0.7 on a BG/P machine (Intrepid at Argonne national lab). The simulated system is a box of SPC water with 648,000 atoms and all MD simulations were performed on 256 CPU cores with MPI. The compiling environment was Linux with IBM compiler and libs. I first compile the code with flags suggested on the Wiki, such as: ./configure --prefix=$PREFIX \ --host=ppc \ --build=ppc64 \ --disable-software-sqrt \ --enable-ppc-sqrt=1 \ n bsp; --enable-ppc-altivec \ The wiki doesn't suggest this, and it's for another architecture entirely. I don't know if it's causing a problem, but you should see what kernels the .log file reports it is trying to use. --enable-bluegene \ --disable-fortran \ --enable-mpi \ --with-fft=fftpack \ This is a waste of a good BlueGene :-) Use FFTW, which has been optimized for BlueGene. [Edit: ah I see why you tried this] --without-x \ CC=mpixlc_r \ CFLAGS=-O3 -qarc h=450d -qtune=450 \ MPICC=mpixlc_r CXX=mpixlcxx_r CXXFLAGS=-O3 -qarch=450 -qtune=450 F77=mpixlf77_r FFLAGS=-O3 -qarch=450 -qtune=450 LIBS=-lmass Here I used fftpack to ensure that the problem is not due to the fftw lib. I got the water system running will with Cut-off for electrostatics. However, the systems always crashed after a few ( ~100) steps if I used PME. The same system with same PME option runs fine on other non-blue gene clusters I tested. The error message I got was sth like t = 0.100 ps: Water molecule starting at atom 403468 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates. and 2 particles communicated to PME node 63 are more than a cell length out of the domain decomposition cell of their charge group From .log file, the kinetic energy is increasing and turned to be nan. So the system is exploding. I found if I turned off the blue gene optimizations during configure, the water system could be run without problem. For example, I used --enable-software-sqrt \ --disable-ppc-sqrt \ --disable-bluegene \ and everything else was the same. I suspect there was an issue regarding the blue gene specific code and PME. Could anyone give any comments? First, try without --enable-ppc-altivec in case that's confusing things. Then try setting the enviroment variable NOASSEMBLYLOOPS to 1 before mdrun to see whether the issue really is specific to the BlueGene-kernel. (Consult mpirun documentation about how to set env vars suitably) You might also try compiling with lower optimization levels, to see if its a compiler/optimization issue. Depending what you find above, there are other things to try. Mark _ SkyDrive电子画册，带你领略精彩照片，分享“美”时“美”刻! http://www.windowslive.cn/campaigns/e-magazine/ngmchina/?a=c-- 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] PMF in vacuum and pull direction
Dear Eudes: This is better, but I'm afraid that I'm going to have to insist on getting everything I asked for. Please see my previous message. Chris. -- original message -- Dear Chris, I'm so sorry for surperficial email. You are correct because in the previous message I forgot to mention that now the simulation was performed in water (naturally with PBC). The main parameters of the simulation are given below. As I said, I wish to keep the displacement of the pulled molecule at the z-axis, but I'm not getting with this protocol. For the vacuum I followed the tips you gave me earlier and had success! Thanks eef title = Umbrella pulling simulation integrator = sd dt = 0.002 nsteps = 300 constraint_algorithm = lincs constraints = all-bonds nstlist = 5 ns_type = simple rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = Cut-off Tcoupl = V-rescale tc_grps = system tau_t = 0.1 ref_t = 298 Pcoupl = no pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 pbc = xyz ; Pull code pull = umbrella pull_geometry = direction pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = BEN1 pull_group1 = BEN2 pull_vec1 = 0 0 1 pull_rate1 = 0.001 pull_k1 = 1600 Message: 4 Date: Tue, 08 Jun 2010 08:05:23 -0400 From: chris.neale at utoronto.ca Subject: [gmx-users] PMF in vacuum and pull direction To: gmx-users at gromacs.org Message-ID: 20100608080523.i6oo62he1wwc0wkg at webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: You can make my job a whole lot easier! First, please go back through all of the comments that I gave you last time and reply to them one by one. Did you do them? What did you see? Second, please include your new .mdp and some quantitative results to better explain what you see (e.g. your .px file and a description of why the values are not what you expect). Sorry if this sounds annoying, but there's no point in my working in the dark. Chris. -- original message -- Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used pull_geometry = direction. However, at the end of the simulation, I notice that the desired alignment (with z) was not maintained. The molecule is pulled away from z and eventually crosses the PBC. I took a good look at gmx-list and noticed that you rode conducting tests with this option. Could you give me a light on this problem too? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC ? CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br Message: 2 Date: Thu, 27 May 2010 12:12:03 -0400 From: chris.neale at utoronto.ca Subject: [gmx-users] PMF in vacuum To: gmx-users at gromacs.org Message-ID: 20100527121203.orb2sq228s4ow0wg at webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and
[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)
Hello Chris, thanks for the reply. Below his message commented walkthrough. In your email you asked me for quantitative results. All I have so far is a visual inspection of the pulling trajectory. All I can see are the two molecules moving linearly away from each other in a rectangular box of dimensions 3x3x6nm. However this separation does not occur on the z axis, as I wanted, but in a diagonal way across the faces of the box. Bests eef 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. Ok, now I'm using only the center of mass of the molecules, no virtual sites. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. Alright! In fact the well of both PMFs are not so different. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. Apesar de eu nao ter incluido o valor do cutoff na mensagem anterior eu usei 1.2 nm Although I have not included the cutoff value in previous message I used it as 1.2 nm. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. A ideia de usar POSRES se referia ao emprego dos sitios virtuais. Assim eu restringia a distancia das moleculas atraves da restricao do sitios virtuais sobre seus centros. The idea of using POSRES is referred to the employment of the virtual sites. So I restricted the distance of molecules by restricting virtual sites on their centers. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. I want to separate the two molecules from one another so that the displacement is restricted to the z axis. I can be wrong, but I think to do it in water, using PBC, I should use the components distance (N N Y ) with direction geometry to get a pulling in a direction z! Please correct me if it is wrong. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? Here they are worthless, because I have not used the option cylinder. I should have removed these options from the original message. ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. Surely. 6. regarding histo.png: can you confirm that the few very short gaussians are due to less sampling in a few windows? In any event, the overlap looks good. Yes, there were two histograms whose simulations had crashed for some reason. It was corrected. ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br 4. PMF in vacuum and pull direction (chris.ne...@utoronto.ca) Message: 4 Date: Tue, 08 Jun 2010 12:14:34 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum and pull direction To: gmx-users@gromacs.org Message-ID: 20100608121434.u6rhqhz400gc8...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: This is better, but I'm afraid that I'm going to have to insist on getting everything I asked for. Please see my previous message. Chris. -- original message -- Dear Chris, I'm so sorry for surperficial email. You are correct because in the previous message I forgot to mention that now the simulation was performed in water (naturally with PBC). The main parameters of the simulation are given below. As I said, I wish to keep the displacement of the pulled molecule at the z-axis, but I'm not getting with this protocol. For the vacuum I followed the tips you gave me earlier and had success! Thanks eef title = Umbrella pulling simulation integrator = sd dt = 0.002 nsteps = 300 constraint_algorithm = lincs constraints = all-bonds nstlist = 5 ns_type = simple rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = Cut-off Tcoupl = V-rescale
Re: [gmx-users] tutorial of free energy calculations
HI Its not working for me either. But for free energy tutorials using GROMACS, I think the one written by Prof Mobley is like Bible. The link is as follows: http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial But the one written by Prof Alan Mark (who is now in Queensland Univ, Australia) is also very useful. Try searching for it. Regards Sai 2010/6/7 fancy2012 fancy2...@yeah.net Dear GMX users, I don't know why I can't open the tutorial of free energy calculations on this website http://www.gromacs.org/Documentation/Tutorials. Can you open it? Thanks very much! All the best, fancy -- 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 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
Re: [gmx-users] 100 step md run: Infinite giga flopses error
Thanks Justin. I think you are right. I always encounter this problem with extremely small runs. On Tue, Jun 8, 2010 at 11:04 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am running a very short md run for 100 steps and I get the Infinite giga flopses error. I stored info at every step to check if the simulation is running. And the log file has all the variables for each time-step with reasonable values. I don't understand the meaning of the message at the end of the log file. nodetime = 0! Infinite Giga flopses! Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 This is not the first time I have encountered this problem with short md runs. This isn't really a problem, per se. Gromacs is fast. If you look at the benchmarks in the Gromacs 4 paper, you can get several hundred steps of MD per second for a relatively small system. So essentially your run probably finished in less than a second, and mdrun recorded that as zero time. Division by zero = infinite performance :) If you think there's something else actually wrong, please at least provide a description of how large your system is, how long the run actually took to complete, if you're running in parallel, etc. -Justin Parameter file ; VARIOUS PREPROCESSING OPTIONS title=NPT simulation for a 2D WCA system cpp =/lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.0001 nsteps = 100 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1 ; Write every nth step to the log nstenergy= 0 ; Write energies at every n step nstxtcout= 0 ; Do not write a compressed tr ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Cut-off rcoulomb = 1.1225 vdw-type = Cut-off rvdw = 1.1225 ; Temperature coupling tcoupl = v-rescale tc-grps = AR tau_t= 0.1 ref_t= 0.1 ld_seed =-1 ; Pressure coupling pcoupl = Berendsen pcoupltype = semiisotropic tau-p= 0.1 0.1 compressibility = 1e-5 0 ;Dont know ref-p= 58 0 ;Generate velocities for startup run gen_vel =yes gen_temp =1 gen_seed =-1 ;Non equilibrium MD steps freezegrps =AR freezedim =N N Y Error: At the end of log file nodetime = 0! Infinite Giga flopses! Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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/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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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
Re: [gmx-users] Thr - Met in TI calculation
Hi Fancy, The following link shows the change from p-cresol to Toluene. So follow the steps in the same by converting threonine to methionine. http://compbio.chemistry.uq.edu.au/education/Free-Energy_Course/0.introduction.html Regards Sai 2010/6/5 fancy2012 fancy2...@yeah.net Dear GMX users, I want to calculate the relative binding free energy between a small molecule binding to a protein of Wild Type and Thr - Met using TI, so how should I prepare the topology files of the protein using for TI calculation? Any suggestions will be highly appreciated? All the best, fancy -- 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 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: thermodynamic integration yields different values..
Dear Gromacs users, it seems what I have stumbled upon is a known bug of Version 3.3.1. Here are the corresponding discussions: http://bugzilla.gromacs.org/show_bug.cgi?id=175 http://www.mail-archive.com/gmx-users@gromacs.org/msg12180.html Best Emanuel -- 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
Re: RE: [gmx-users] PME problem on BG/P cluster
- Original Message -
From: LuLanyuan lulany...@msn.com
Date: Wednesday, June 9, 2010 2:10
Subject: RE: [gmx-users] PME problem on BG/P cluster
To: gmx-users@gromacs.org
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Dear Mark,
When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any
problem. So I guess it's related to the assembly loops for BG.
OK, that's useful data. I understand that these loops are believed to work on
BG/P. Knowing the code, I can think of no reason why the problem should be
BG/P-specific. Please open a http://bugzilla.gromacs.org report, CC my email
address, and attach your .tpr, and I'll try it on my BG/L.
I actually have well-tested ready-to-release updates to these kernels that
perform up to about 10% better on PME on BG/L. Depending what we find above,
and if you're interested, I could let you try them on BG/P, since I don't have
the ability to test on BG/P.
Mark
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Sat, 5 Jun 2010 03:31:33 +1000
Subject: Re: [gmx-users] PME problem on BG/P cluster
- Original Message -
From: LuLanyuan lulany...@msn.com
Date: Saturday, June 5, 2010 2:01
Subject: [gmx-users] PME problem on BG/P cluster
To: gmx-users@gromacs.org
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Hello,
I got a weird problem by running Gromacs 4.0.7 on a BG/P machine
(Intrepid at Argonne national lab).
The simulated system is a box of SPC water with 648,000 atoms and all MD
simulations were performed on 256 CPU cores with MPI. The compiling
environment was Linux with IBM compiler and libs.
I first compile the code with flags suggested on the Wiki, such as:
./configure --prefix=$PREFIX \
--host=ppc \
--build=ppc64 \
--disable-software-sqrt \
nbsp; --enable-ppc-sqrt=1 \
n bsp; --enable-ppc-altivec \
The wiki doesn't suggest this, and it's for another architecture entirely. I
don't know if it's causing a problem, but you should see what kernels the
.log file reports it is trying to use.
--enable-bluegene \
n bsp; --disable-fortran \
--enable-mpi \
--with-fft=fftpack \
This is a waste of a good BlueGene :-) Use FFTW, which has been optimized for
BlueGene. [Edit: ah I see why you tried this]
--wit hout-x \
nbs p; CC=mpixlc_r \
CFLAGS=-O3 -qarc h=450d -qtune=450 \
MPICC=mpixlc_r
CXX=mpixlcxx_r
CXXFLAGS=-O3 -qarch=450 -qtune=450
F77=mpixlf77_r
FFLAGS=-O3 -qarch=450 -qtune=450
LIBS=-lmass
Here I used fftpack to ensure that the problem is not due to the fftw lib.
I got the water system running will with Cut-off for electrostatics.
However, the systems always crashed after a few ( ~100) steps if I used
PME. The same system with same PME option runs fine on other non-blue gene
clusters I tested.
The error message I got was sth like
t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates.
and
2 particles communicated to PME node 63 are more than a cell length out of
the domain decomposition cell of their charge group
/fontFrom .log file, the kinetic energy is increasing and turned to be
nan. So the system is exploding.
I found if I turned off the blue gene optimizations during configure, the
water system could be run without problem. For example, I used
--enable-software-sqrt \
- -disable-ppc-sqrt \
--disable-bluegene \
and everything else was the same.
I suspect there was an issue regarding the blue gene specific code and PME.
Could anyone give any comments?
First, try without --enable-ppc-altivec in case that's confusing things. Then
try setting the enviroment variable NOASSEMBLYLOOPS to 1 before mdrun to see
whether the issue really is s pecific to the BlueGene-kernel. (Consult
mpirun documentation about how to set env vars suitably) You might also try
compiling with lower optimization levels, to see if its a
compiler/optimization issue. Depending what you find above, there are other
things to try.
Mark
|
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[gmx-users] Reduced LJ Units
Hi, I have trouble searching mailing lists so I apologize if this has already been answered in some query. If sigma=epsilon=mass=1 is specified in .top file then for specifying T*=1 in the Thermostat does one need to set ref_t ~ 120 ? Similarly, to specify ref_p for the Barostat, is there a similar conversion factor? How about the values of P reported in bar? How does one convert that to reduced units? I ask this because I have currently specified ref_t =120 as explained in the Gromacs manual. However this gives me a pressure value(in bars) which is much much larger than the one I had expected in reduced units (by a factor of about 50-60). -Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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
Re: [gmx-users] Reduced LJ Units
- Original Message - From: Sai Pooja saipo...@gmail.com Date: Wednesday, June 9, 2010 8:07 Subject: [gmx-users] Reduced LJ Units To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I have trouble searching mailing lists so I apologize if this has already been answered in some query. If sigma=epsilon=mass=1 is specified in .top file then for specifying T*=1 in the Thermostat does one need to set ref_t ~ 120 ? Similarly, to specify ref_p for the Barostat, is there a similar conversion factor? How about the values of P reported in bar? How does one convert that to reduced units? Does manual table 2.4 help? I ask this because I have currently specified ref_t =120 as explained in the Gromacs manual. However this gives me a pressure value(in bars) which is much much larger than the one I had expected in reduced units (by a factor of about 50-60). Are you measuring pressure over long enough time? See http://www.gromacs.org/Documentation/Terminology/Pressure Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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
RE: [gmx-users] PME problem on BG/P cluster
Thanks, Mark. I've post it on the bugzilla. I'm glad to try the new assembly loops on BG/P as well. Lanyuan From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Date: Wed, 9 Jun 2010 07:48:26 +1000 Subject: Re: RE: [gmx-users] PME problem on BG/P cluster - Original Message - From: LuLanyuan lulany...@msn.com Date: Wednesday, June 9, 2010 2:10 Subject: RE: [gmx-users] PME problem on BG/P cluster To: gmx-users@gromacs.org Dear Mark, When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any problem. So I guess it's related to the assembly loops for BG. OK, that's useful data. I understand that these loops are believed to work on BG/P. Knowing the code, I can think of no reason why the problem should be BG/P-specific. Please open a http://bugzilla.gromacs.org report, CC my email address, and attach your .tpr, and I'll try it on my BG/L. I actually have well-tested ready-to-release updates to these kernels that perform up to about 10% better on PME on BG/L. Depending what we find above, and if you're interested, I could let you try them on BG/P, since I don't have the ability to test on BG/P. Mark From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Date: Sat, 5 Jun 2010 03:31:33 +1000 Subject: Re: [gmx-users] PME problem on BG/P cluster - Original Message - From: LuLanyuan lulany...@msn.com Date: Saturday, June 5, 2010 2:01 Subject: [gmx-users] PME problem on BG/P cluster To: gmx-users@gromacs.org Hello, I got a weird problem by running Gromacs 4.0.7 on a BG/P machine (Intrepid at Argonne national lab). The simulated system is a box of SPC water with 648,000 atoms and all MD simulations were performed on 256 CPU cores with MPI. The compiling environment was Linux with IBM compiler and libs. I first compile the code with flags suggested on the Wiki, such as: ./configure --prefix=$PREFIX \ --host=ppc \ --build=ppc64 \ --disable-software-sqrt \ nbsp; --enable-ppc-sqrt=1 \ n bsp; --enable-ppc-altivec \ The wiki doesn't suggest this, and it's for another architecture entirely. I don't know if it's causing a problem, but you should see what kernels the .log file reports it is trying to use. --enable-bluegene \ n bsp; --disable-fortran \ --enable-mpi \ --with-fft=fftpack \ This is a waste of a good BlueGene :-) Use FFTW, which has been optimized for BlueGene. [Edit: ah I see why you tried this] --wit hout-x \ nbs p; CC=mpixlc_r \ CFLAGS=-O3 -qarc h=450d -qtune=450 \ MPICC=mpixlc_r CXX=mpixlcxx_r CXXFLAGS=-O3 -qarch=450 -qtune=450 F77=mpixlf77_r FFLAGS=-O3 -qarch=450 -qtune=450 LIBS=-lmass Here I used fftpack to ensure that the problem is not due to the fftw lib. I got the water system running will with Cut-off for electrostatics. However, the systems always crashed after a few ( ~100) steps if I used PME. The same system with same PME option runs fine on other non-blue gene clusters I tested. The error message I got was sth like t = 0.100 ps: Water molecule starting at atom 403468 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates. and 2 particles communicated to PME node 63 are more than a cell length out of the domain decomposition cell of their charge group /fontFrom .log file, the kinetic energy is increasing and turned to be nan. So the system is exploding. I found if I turned off the blue gene optimizations during configure, the water system could be run without problem. For example, I used --enable-software-sqrt \ - -disable-ppc-sqrt \ --disable-bluegene \ and everything else was the same. I suspect there was an issue regarding the blue gene specific code and PME. Could anyone give any comments? First, try without --enable-ppc-altivec in case that's confusing things. Then try setting the enviroment variable NOASSEMBLYLOOPS to 1 before mdrun to see whether the issue really is s pecific to the BlueGene-kernel. (Consult mpirun documentation about how to set env vars suitably) You might also try compiling with lower optimization levels, to see if its a compiler/optimization issue. Depending what you find above, there are other things to try. Mark 聊天+搜索+邮箱 想要轻松出游,手机MSN帮你搞定! 立刻下载！ -- 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
Re: [gmx-users] Reduced LJ Units
Thanks Mark. I looked at the link you has sent. However, with pressure coupling I haven't seen such fluctuations for my system. The pressure value is the one obtained at the end of a long NPT simulation - 10^8 steps with dt=10^-4. The rms fluctuations in pressure are small, of the order of 1-0.1 bar. On Tue, Jun 8, 2010 at 6:34 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Wednesday, June 9, 2010 8:07 Subject: [gmx-users] Reduced LJ Units To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I have trouble searching mailing lists so I apologize if this has already been answered in some query. If sigma=epsilon=mass=1 is specified in .top file then for specifying T*=1 in the Thermostat does one need to set ref_t ~ 120 ? Similarly, to specify ref_p for the Barostat, is there a similar conversion factor? How about the values of P reported in bar? How does one convert that to reduced units? Does manual table 2.4 help? I ask this because I have currently specified ref_t =120 as explained in the Gromacs manual. However this gives me a pressure value(in bars) which is much much larger than the one I had expected in reduced units (by a factor of about 50-60). Are you measuring pressure over long enough time? See http://www.gromacs.org/Documentation/Terminology/Pressure Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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
Re: [gmx-users] PBC
Hi Morteza, I had this problem when I was running a trimeric protein attached to an oligosaccharide. *I have used the following command:* * * *trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol* * * *but it is not working.* Do the following. It worked for me. In the first round, run trjconv -f *.xtc -s *.tpr -center -boxcenter tric -pbc mol -o 1.xtc and choose backbone (which is usually 4 from the index) for centring. In the second round, use 1.xtc obtained from the first step and run the command as follows trjconv -f 1.xtc -s *.tpr -center -boxcenter tric -pbc a -o 2.xtc and this time also choose the backbone for centring. This should bring back the dimeric protein system in the box. Sometimes the water molecules around the edge are broken. Hope this is not a big worry. By the way is your box cubic or truncated octahedron? My case was a cubic box. Hope this helps. Regards Sai On Tue, Jun 8, 2010 at 2:23 AM, shahab shariati shahab.shari...@gmail.comwrote: Morteza Khabiri wrote: Dear users I have a dimer protein in the water box. It was run for 30ns. during the simulation dimer split to two monomer. This things happen bc of PBC. ( I checked it by vmd pbc option ) to have a two monomer together during trajectories (for visualization) I have used the following command: trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol but it is not working. Is there any other method or command which I could implement pbc in trajectory. Thanks in advance Morteza Shahab Shariati wrote: You can use other flags of trjconv command as follows: Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center -- 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 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] PMF in vacuum and pull direction
Dear Eudes: Thanks for working with me on this one! What you are getting is actually what you are asking for in your .mdp file. You restrain the Z-projection of the displacement, but do not affect the X and Y components of the displacement with pull_dim = N N Y. If you want to pull with separation only in z and want the x and y components of the displacement to be close to zero, then you want pull_dim = Y Y Y. Let's be clear: you say I should use the components distance (N N Y ) with direction geometry to get a pulling in a direction z! Please correct me if it is wrong.. And you are literally correct that you should set pull_dim = N N Y if you only want to pull in z, by which we mean that you only want to apply a biasing force based on the z component of the displacement. But what it seems that you want to do is to pull only in z but also to add a constant bias in x and y such that their displacement component remains close to zero. Now I'm not entirely sure what you want to do, but to me the following seems like it will do what you want: ; Pull code pull = umbrella pull_geometry = direction pull_dim = Y Y Y pull_start = yes pull_ngroups = 1 pull_group0 = BEN1 pull_group1 = BEN2 pull_vec1 = 0 0 1 pull_rate1 = 0.001 pull_k1 = 1600 Note that I only changed your pull_dim. Chris. -- original message -- Hello Chris, thanks for the reply. Below his message commented walkthrough. In your email you asked me for quantitative results. All I have so far is a visual inspection of the pulling trajectory. All I can see are the two molecules moving linearly away from each other in a rectangular box of dimensions 3x3x6nm. However this separation does not occur on the z axis, as I wanted, but in a diagonal way across the faces of the box. Bests eef 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. Ok, now I'm using only the center of mass of the molecules, no virtual sites. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. Alright! In fact the well of both PMFs are not so different. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. Apesar de eu nao ter incluido o valor do cutoff na mensagem anterior eu usei 1.2 nm Although I have not included the cutoff value in previous message I used it as 1.2 nm. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. A ideia de usar POSRES se referia ao emprego dos sitios virtuais. Assim eu restringia a distancia das moleculas atraves da restricao do sitios virtuais sobre seus centros. The idea of using POSRES is referred to the employment of the virtual sites. So I restricted the distance of molecules by restricting virtual sites on their centers. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. I want to separate the two molecules from one another so that the displacement is restricted to the z axis. I can be wrong, but I think to do it in water, using PBC, I should use the components distance (N N Y ) with direction geometry to get a pulling in a direction z! Please correct me if it is wrong. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? Here they are worthless, because I have not used the option cylinder. I should have removed these options from the original message. ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. Surely. 6. regarding histo.png: can you confirm that the few very short gaussians are due to less sampling in a few windows? In any event, the overlap looks good. Yes, there were two histograms whose simulations had crashed for some reason. It was corrected. -- 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!
Re: [gmx-users] building long polymer chain
Moeed wrote: Hello Justin, I am trying to generate the top file for polyethylene chain using the information from the archive: http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html. In the former post you said parameters in the I am referring to are not necessarily correct. 1- By parameters you mean the coordinates in pdb file? The residues in this link seem correct to me but I am not sure if the hdb file is correct. The term parameters refers to atom types and charges. The example I created for the post above is based on what I believed to be plausible atom types and charges for alkyl groups, but I have never validated these items for use in polymers. The post was to be instructive only. Maybe the parameters are suitable, maybe they are not. 2- Could you please tell me how to generate a longer chain with the given residue types proposed in the above post. ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 EthE3 3.912 5.623 0.000 ATOM 6 C2 EthE3 5.368 6.124 0.000 END Here I do not see hydrogen atoms. I have created a long chain with 100 monomer units using Ascalaph designer. However the file is not properly formatted. i.e atoms are not numbered and residue name is missing. I do not want to alter the file by hand. Can you guide me how I can build a long chain with the residues you proposed in the above post (including hydrogen atoms) The residues I created assume that there are corresponding entries in the appropriate .hdb file, which I provided in the post you quote. As for creating a coordinate file: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources HETATM1 C 1 2.739 2.554 -0.012 -0.390 C HETATM2 H 1 2.736 3.644 -0.012 0.130 H HETATM3 H 1 2.190 2.217 -0.893 0.130 H HETATM4 H 1 2.190 2.217 0.868 0.130 H HETATM5 C 2 4.155 1.993 -0.012 -0.260 C . . HETATM 291 H 97 72.086 -97.891 -0.012 0.130 H HETATM 292 H 97 70.558 -97.880 0.869 0.130 H HETATM 293 H 97 70.558 -97.880 -0.893 0.130 H 3- I have also an inquiry about the density of my solvent. One of the experts told me: Best thing you can do is, make a NPT simulation (look for the right compresibility) and look how much your density is off,if it's only a little your fine. I dont realize the statement look how much your density is off? The desnity is approx. 71000 Kg/m3 (4molecuels per nm3). From NPT run I see the density is 577 Kg/m3. and the volume is 30 nm3 (values from g_energy). How can I make sure if density changes are reasonable? You need experimentally-derived densities to compare your values. To what does 71000 kg/m^3 correspond? If that's your target value, you're nowhere close. For polyethylene, the density depends on the molecular weight and geometry, correct? The target value should depend upon what you're trying to model. -Justin *Volume * 30.9568* 0.374111 0.204815 Density (SI)*577.914*6.978043.80252 Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.366 12.08611.40211.38812 13.884 Pressure (bar) -30.0299746.524745.665 -12.3992 -124.017 *Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449* ** *Density (SI)577.9146.978043.802522.02643 20.2684* pV -55.98791393.391391.81 -22.9985 -230.031 #Surf*SurfTen218.214871.454871.37 -9.30662 -93.0848 T-HEX 297.366 12.08611.40211.38812 13.884 Lamb-HEX1.00011 0.000588089 0.000561362 -6.07045e-05 -0.000607166 Heat Capacity Cv: 12.5027 J/mol K (factor = 0.0016519) Isothermal Compressibility: 0.00011012 /bar Adiabatic bulk modulus:9080.99 bar with mdp file: ;Pressure coupling: Pressure coupling is not on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Thanks, -- 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] Position restrained Dynamics
Hi All, I am trying to simulate kinase domain (chain A) in complex with cyclin (chain B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need to keep only kinase domain flexible but cyclin fixed. i put POSRES_B in define variable and tried to simulated the entire solvated system in GROMACS 4 package. But time and again it failed with LINCS warnings. On the contrary, if entire system is kept either flexible or position restrained, run is obtained without any errors. I tried 1ns MD. Unable to understand possible reasons. Could anybody help in this regard ? Regards, Nikhil -- 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
