RE： [gmx-users] A very strang e problem about version of pdb2gmx
Dear gmxers, I have reinstalled the gmx-4.5.1 and this time the pdb2gmx is found to work using the same input and parameter files. So I consider that the very strange problem is due to some modified file which is unknown yet for me. Thanks again for your attention. Sincerely, yours Chaofu Wu, Dr. -- 原始邮件 -- 发件人: Justin A. Lemkuljalem...@vt.edu; 发送时间: 2010年10月17日(星期天) 晚上8:21 收件人: Discussion list for GROMACS usersgmx-users@gromacs.org; 主题: Re: [gmx-users] A very strange problem about version of pdb2gmx 英雄不再寂寞 wrote: Dear gmxers, Yesterday, I posted a mail titled pdb2gmx stop at AtomType 1 where I mentioned that I used gmx-4.5.1. The resulting problem is again posted below. Today, I turn to the gmx-4.0.7, and use the same pdb and rtp files with the name modified to compatible to the version. Strangely, it is found that the pdb2gmx of this version can generate the top file without any errors. Could you give me clues to why the latest version can not whereas the older version can? To get the clear help, my pdb and rtp files are also posted below. Thanks a lot for any reply. Your system works for me under version 4.5.1, after fixing the naming mismatch you have between your .pdb file (MOL) and .rtp file (DET). I suppose your actual input files have the correct names, though, otherwise this combination would have generated a fatal error, not a hang. -Justin Chaofu Wu, Dr. My command line and the screen output: xiaowu...@linux-s38y:~/workshop mailto:xiaowu...@linux-s38y:~/workshop pdb2gmx -f deta.pdb -o deta.gro -p deta.top -i deta.itp -ter :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.5.1 (-: .. Opening force field file oplsaa.ff/aminoacids.r2b Reading deta.pdb... Read 20 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 1 residues with 20 atoms chain #res #atoms 1 ' ' 1 20 All occupancies are one Opening force field file oplsaa.ff/atomtypes.atp Atomtype 1 My pdb file: ATOM 1 N1 MOL 1 -5.199 1.343 0.334 1.00 0.00 N ATOM 2 C2 MOL 1 -4.582 0.639 1.470 1.00 0.00 C ATOM 3 C3 MOL 1 -3.897 1.462 2.593 1.00 0.00 C ATOM 4 N4 MOL 1 -3.194 0.615 3.574 1.00 0.00 N ATOM 5 C5 MOL 1 -2.373 1.331 4.566 1.00 0.00 C ATOM 6 C6 MOL 1 -1.520 0.397 5.464 1.00 0.00 C ATOM 7 N7 MOL 1 -0.684 1.133 6.432 1.00 0.00 N ATOM 8 H12 MOL 1 -4.614 2.067 -0.035 1.00 0.00 H ATOM 9 H11 MOL 1 -6.128 1.694 0.483 1.00 0.00 H ATOM 10 H22 MOL 1 -3.826 -0.053 1.056 1.00 0.00 H ATOM 11 H21 MOL 1 -5.345 -0.016 1.926 1.00 0.00 H ATOM 12 H31 MOL 1 -4.628 2.144 3.065 1.00 0.00 H ATOM 13 H32 MOL 1 -3.141 2.116 2.124 1.00 0.00 H ATOM 14 H41 MOL 1 -3.854 0.018 4.043 1.00 0.00 H ATOM 15 H51 MOL 1 -2.980 2.003 5.204 1.00 0.00 H ATOM 16 H52 MOL 1 -1.679 1.992 4.016 1.00 0.00 H ATOM 17 H62 MOL 1 -0.857 -0.180 4.795 1.00 0.00 H ATOM 18 H61 MOL 1 -2.188 -0.346 5.939 1.00 0.00 H ATOM 19 H72 MOL 1 -0.023 0.541 6.916 1.00 0.00 H ATOM 20 H71 MOL 1 -1.253 1.554 7.143 1.00 0.00 H TER My rtp file: [ DET ] [ atoms ] N1opls_900-0.900 1 H11opls_909 0.360 1 H12opls_909 0.360 1 C2opls_906 0.060 1 H21opls_911 0.060 1 H22opls_911 0.060 1 C3opls_907 0.080 2 H31opls_911 0.060 2 H32opls_911 0.060 2 N4opls_901-0.780 2 H41opls_910 0.380 2 C5opls_907 0.080 2 H51opls_911 0.060 2 H52opls_911 0.060 2 C6opls_906 0.060 3 H61opls_911 0.060 3 H62opls_911 0.060 3 N7opls_900-0.900 3 H71opls_909 0.360 3 H72opls_909 0.360 3 [ bonds ] N1 H11 N1 H12 N1C2 C2 H21 C2 H22 C2C3 C3 H31 C3 H32 C3N4 N4 H41 N4C5 C5 H51 C5 H52 C5C6 C6 H61 C6 H62 C6N7 N7 H71 N7 H72 --
Re: [gmx-users] g_dipole ? = dipole moment ?
On 2010-10-19 02.01, Chih-Ying Lin wrote: Hi From David = dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. 1. What does the coefficient 48.0 represent? Unit conversion from e nm to D. 2. Is q_i = partial charge or charge on the atoms / united atoms? 3. Is x_i = the distance between the mass center of atom from the mass center of the molecule? 4. What does the large charge separation mean? Do you mean the charged molecule? Or, Do you mean the molecule with a long carbon chain? Please do a calculation on paper and you will understand. Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position_restraints
Hi, Fatal error: [ file protein.itp, line 9 ]: Atom index (5) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. Thanks for any clue. The part belongs to the one I want to restraints. I mean, the molecule is right. Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Energy Minimization
Hi, I would allow flexible water by uncommenting the line define = -DFLEXIBLE and trying again; reducing the time step might also be required. Message: 4 Date: Mon, 18 Oct 2010 16:26:16 -0400 From: Sai Pooja saipo...@gmail.com Subject: [gmx-users] Energy Minimization To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktinomj-hzw2u+g6sa=mxqlc7q6ibwwiqj+mx6...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi all, I am using CHARMM forcefield with tables for Protein SOL interactions for alanine dipeptide. Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard tables for 6-12 interactions used) Combination rule changed from '2' to '1' in forcefield.itp file. In the energy minimization step, using mdrun the following problem is encountered: Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e+00 Number of steps=1 F-max = 2.98523e+10 on atom 4 F-Norm= 1.32072e+09 step -1: Water molecule starting at atom 1149 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes ;define = -DFLEXIBLE define = -DPOSRES ; Parameters describing what to do, when to stop and what to save integrator = cg; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 1 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = Protein SOL energygrp_table = Protein SOL ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = User ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) Any suggestions? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101018/355f3a 45/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 78, Issue 132 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole ? = Calculate bond dipole moment for a molecule of multiple atoms by hand?
Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +δ — δ- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +δ and δ-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Computational Biomolecular Chemistry Group, Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones
On 18/10/10 13:06, Mark Abraham wrote: On 18/10/2010 10:53 PM, ms wrote: On 18/10/10 03:30, Mark Abraham wrote: Mark, Thanks a lot for cc'ing me the bugzilla report. Do you think it is related to the problems I have? (well, for sure bugs can't help, but...) thank you! m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gibbs free energy of binding
Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs libraries: same for both single and double precision builds?
Hi, I'm installing GROMACS 4.5.1 on our Intel Nehalem/InfiniBand cluster and wish to install both single and double precision versions. Am I correct in thinking that the same libraries are built, both with or without --enable-double, and it's just the binaries that are different (and therefore all packaging issues are solved by use of the --program-suffix option)? I'm planning on building both precisions in the same install - possibly with --enable-shared - and I want to double-check I can use the same library files. Thanks, Mark -- - Mark Dixon Email: m.c.di...@leeds.ac.uk HPC/Grid Systems Support Tel (int): 35429 Information Systems Services Tel (ext): +44(0)113 343 5429 University of Leeds, LS2 9JT, UK - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position_restraints
#ZHAO LINA# wrote: Hi, Fatal error: [ file protein.itp, line 9 ]: Atom index (5) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. As the error message indicates, your #include statement is in the wrong place. In the topology, order matters. The [position_restraints] directive must be #included after the relevant [moleculetype] directive, and not after anything else. -Justin Thanks for any clue. The part belongs to the one I want to restraints. I mean, the molecule is right. Thanks, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gibbs free energy of binding
shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: for gromacs
As I say continually, I am not a private tutor. Please keep all Gromacs-related correspondence on the gmx-users list. I am CC'ing this message there and would ask that any further discussion be held in this forum. Binding energy is not trivial to calculate, and will require some type of free energy calculation (thermodynamic cycles, potential of mean force, etc). Breakdown of short-range nonbonded terms can be accomplished by using the energygrps keyword in the .mdp file. If you've already done your simulation, you'll have to use the mdrun -rerun function with a new .tpr file that has these groups defined. -Justin rajender verma wrote: dear sir I have done MD study of a complex compound (protein-Ligand). I want to calculate the Binding and breakdown energy with protein- ligand. pllease help me sir Thanks -- Rajender Kumar Senior Research Fellow National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S.A.S. Nagar. 160062, Punjab, INDIA http://bioinfoindia.weebly.com/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gibbs free energy of binding
Shahab, Justin is entirely correct, you should read about potential of mean force calculations, the gromacs pull code, and the gromacs free energy code. However, an important question is if you can *converge* the free energy of macromolecular binding. If you don't know the bound state, then I am sure that you can not. I think that it is even unlikely if you do know the bound state. I suggest that you start by calculating the Gibbs free energy of a sodium ion binding to DNA. If you run the entire calculation in duplicate, but starting from different configurations, you should get a flavour of convergence difficulties and methods that you can apply to enhance your convergence. Chris. shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] amb2gmx.pl script ignores negative values of PK?
Hi all,
There is a problem that I encountered when I was trying to manually
verify the proper dihedral conversion from AMBER topology to GROMACS
topology using amb2gmx perl script.
Some of the dihedrals were set to zero by amb2gmx even if in the
prmtop file they were not zero. This was happening for all the lines
that had PK with negative values!. Reading the script I came up with
the following lines for V[i] calculation (lines 749 to 755 in the
script file):
...
# get all force constants for each line of a dihedral #
my $lines = $i -1 +$numijkl;
for(my $j=$i;$j=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}0) {
$V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}
...
It seems from here that only PK values 0 are considered when
computing the RB constants.
After I change the sign to != (i.e. not equal to) everything
goes fine and ALL the dihedral are transformed correctly.
While this is OK with different AMBER sets and GAFF if one wish to
convert a GLYCAM (which comes also with Amber package) generated
topology, in the gromacs resultant file there will be missing
parameters for dihedrals. That's because GLYCAM does not use phase
shift and have also negative values for several PK
Is this a bug or there is a reason for considering only the positive
values of PK or I am missing something (as I am a begginer with
AMBER)?
(or maybe amb2gmx was designed only to work an AMBER ff conversion and
not for example GLYCAM)
Thanks for any comment,
Andrei
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[gmx-users] COM Pulling - Single Chain
Hi All, I was wondering if it is possible to pull on a single chain? I would like to anchor the C-terminus and pull the N-terminus and have a plot of pulling force vs displacement. I'm looking for more or less a yes or no answer, if you would like to elaborate then I won't complain :) Thanks, Joe -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] COM Pulling - Single Chain
yes. use the pull code. check your convergence carefully. --original message -- Hi All, I was wondering if it is possible to pull on a single chain? I would like to anchor the C-terminus and pull the N-terminus and have a plot of pulling force vs displacement. I'm looking for more or less a yes or no answer, if you would like to elaborate then I won't complain :) Thanks, Joe -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/625c900f/attachment.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella sampling with temperature and pressure coupling method problem
Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella sampling with temperature and pressure coupling method problem
Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but probably you need to provide more information to get a useful answer there. -- original message -- Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun-gpu error
Hi Roland, I did as you suggested and it worked fine! Thanks, Renato 2010/10/15 Roland Schulz rol...@utk.edu: You should use the latest GROMACS version also for the GPU. Thus compile the 4.5.1 for the GPU and run this. On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas renato...@gmail.com wrote: Hi there, I have installed the gromacs-4.5.1 and it was running without problems. Also I installed the GPU version of GROMACS (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and NVIDIA driver are installed. Then I tried to run the test provided by Alan with the mdrun-gpu and I got an error. # To test mdrun-gpu cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol = 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md-vv nsteps = 1000 dt = 0.002 constraints = all-bonds constraint-algorithm = shake nstcomm = 1 nstcalcenergy = 1 ns_type = grid rlist = 1.3 rcoulomb = 1.3 rvdw = 1.3 vdwtype = cut-off coulombtype = PME Tcoupl = Andersen nsttcouple = 1 tau_t = 0.1 tc-grps = system ref_t = 300 Pcoupl = mttk Pcoupltype = isotropic nstpcouple = 1 tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF wget -c http://www.pdbe.org/download/1brv;; -O 1brv.pdb pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0 genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p Prot.top -norandom grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr mdrun-gpu -v -deffnm md -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes --- Getting Loaded... Reading file md.tpr, VERSION 4.5 (single precision) --- Program mdrun-gpu, VERSION 4.5-GPU-beta2 Source code file: /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c, line: 1971 Fatal error: reading tpx file (md.tpr) version 73 with version 71 program For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I also have tried to use my own system to test the mdrun-gpu and I got the same error. Any ideas? Thanks, Renato -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] COM Pulling - Single Chain
Maybe I'm confused here, but the manual says that the pull code will not in general work for groups that have other constraints. To quote the last part of section 6.3: There is one important limitation: strictly speaking, constraint forces can only be calculated between groups that are not connected by constraints to the rest of the system. If a group contains part of a molecule of which the bondlengths are constrained, the pull constraint and LINCS or SHAKE bond constraint algorithms should be iterated simultaneously. This is not done in GROMACS. This means that for simulations with constraints = all-bonds in the .mdp file pulling is, strictly speaking, limited to whole molecules or groups of molecules. In some cases this limitation can be avoided by using the free energy code, see sec. 6.4. In practice the errors caused by not iterating the two constraint algorithms can be negligble when the pull group consists of a large amount of atoms and/or the the pull force is small. In such cases the constraint correction displacement of the pull group is small compared to the bond lengths. So it sounds like you might be OK if you use a small pull force. The free energy code is also problematic for measuring the forces because it creates a cycle of constraints, which yields an occasional but problematic spike to huge values when trying to calculate the free energy as a function of end-to-end distance of a peptide. Warren Gallin On 2010-10-19, at 6:50 AM, chris.ne...@utoronto.ca wrote: yes. use the pull code. check your convergence carefully. --original message -- Hi All, I was wondering if it is possible to pull on a single chain? I would like to anchor the C-terminus and pull the N-terminus and have a plot of pulling force vs displacement. I'm looking for more or less a yes or no answer, if you would like to elaborate then I won't complain :) Thanks, Joe -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/625c900f/attachment.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] COM Pulling - Single Chain
Warren, You're right that one can not use constraints if they are also using lincs on C-C bonds. However, constraining this bond is not necessary with a 1 fs timestep. Even while constraining C-C bond lengths, one can still use harmonic restraints instead (also from the pull code). Before getting any more specific replies, Joe will likely need to provide a whole bunch more information about what he wants to do, what he has tried, what problem he has run into, etc. Chris. -- original message -- Maybe I'm confused here, but the manual says that the pull code will not in general work for groups that have other constraints. To quote the last part of section 6.3: There is one important limitation: strictly speaking, constraint forces can only be calculated between groups that are not connected by constraints to the rest of the system. If a group contains part of a molecule of which the bondlengths are constrained, the pull constraint and LINCS or SHAKE bond constraint algorithms should be iterated simultaneously. This is not done in GROMACS. This means that for simulations with constraints = all-bonds in the .mdp file pulling is, strictly speaking, limited to whole molecules or groups of molecules. In some cases this limitation can be avoided by using the free energy code, see sec. 6.4. In practice the errors caused by not iterating the two constraint algorithms can be negligble when the pull group consists of a large amount of atoms and/or the the pull force is small. In such cases the constraint correction displacement of the pull group is small compared to the bond lengths. So it sounds like you might be OK if you use a small pull force. The free energy code is also problematic for measuring the forces because it creates a cycle of constraints, which yields an occasional but problematic spike to huge values when trying to calculate the free energy as a function of end-to-end distance of a peptide. Warren Gallin On 2010-10-19, at 6:50 AM,chris.neale at utoronto.ca http://lists.gromacs.org/mailman/listinfo/gmx-users wrote: / yes. use the pull code. check your convergence carefully. // // --original message -- // // Hi All, // // I was wondering if it is possible to pull on a single chain? I would like to anchor the C-terminus and pull the N-terminus and have a plot of pulling force vs displacement. // // I'm looking for more or less a yes or no answer, if you would like to elaborate then I won't complain :) // // Thanks, // Joe / -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)
Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Umbrella sampling with temperature and pressurecoupling method problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cbd9d87.6080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed chris.ne...@utoronto.ca wrote: Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but probably you need to provide more information to get a useful answer there. The Berendsen barostat suffers from the same limitations as the thermostat - the pressure distribution does not produce a true NPT ensemble. Whether the correct canonical ensemble (NPT or NVT) is important (or indispensable) for umbrella sampling? If I used the weak coupling method (Berendsen) to do the simulations, can I extract the PMF from the umbrella sampling simulations? -Justin -- original message -- Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Point Dipoles
Hi Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole to a molecule with an orientation? I've looked in the manual but find nothing or online. Also is there any provision for SSD [soft sticky dipole] water molecules? Thanks Brett-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Point Dipoles
On 2010-10-19 18.40, Donovan B.T. wrote: Hi Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole to a molecule with an orientation? I've looked in the manual but find nothing or online. Also is there any provision for SSD [soft sticky dipole] water molecules? No analytical dipoles. Would be nice to have. Thanks Brett-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)
DeChang Li wrote: Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Umbrella sampling with temperature and pressurecoupling method problem To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4cbd9d87.6080...@vt.edu mailto:4cbd9d87.6080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but probably you need to provide more information to get a useful answer there. The Berendsen barostat suffers from the same limitations as the thermostat - the pressure distribution does not produce a true NPT ensemble. Whether the correct canonical ensemble (NPT or NVT) is important (or indispensable) for umbrella sampling? If I used the weak coupling method (Berendsen) to do the simulations, can I extract the PMF from the umbrella sampling simulations? I would think that a proper statistical mechanical ensemble would be considered indispensable for any simulation. In my mind, there is no real reason to use less accurate methods when collecting data. If your goal is a comparison of methods, or consistency with other results, sure, then you may have a reason to use algorithms that may be less than optimal. For any sensitive thermodynamic study, I would strongly argue that your potential energy surface needs to be rigorously correct. The point is this. You have to defend your choices to a skeptical audience (reviewers). This is one question that might be asked, and really should be. Methods should be scrutinized. So I would ask you this: why perform your simulations with algorithms that are not as accurate as others, when those better algorithms are accessible to you and do not harm performance in any demonstrable way? -Justin -Justin -- original message -- Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? Here, I attached the perl script I used. Thanks. Regards, Joyce top2psf.pl Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:14:34 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- 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 mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tables with forcefield
On 27/09/10 21:18, Sai Pooja wrote: Thanks M! I am using the standard 6-12 tables available with the gromacs package. For -table and -tablep options to start with. I want to understand 1 thing. The forcefield files and the topology file specifies sigma and epsilon parameters. If I change the combination rule to 1 in the forcefield.itp file, and use tables, how does gromacs convert the sigma, epsilon values in the topology file to C6 and C12? This is explained in the manual. specificially section 6.7.2 -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Template file in gromacs4.5.1
Hi I had developed couple of post processing/analysis codes in earlier version of gromacs4.0.7. Now I have upgraded to gromacs4.5.1 and when I check its template file , its completely different that the earlier version. Does that mean old post-processing codes have to rewritten if I were to use new gromacs? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Template file in gromacs4.5.1
Also, will there be any errors if I use trajectory computed by gromacs4.5.1 and use post processing code developed for gromacs4.0.7. I plan to keep both versions of gromacs installed on my system, until I get fully comfortable new version! On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak symasha...@gmail.comwrote: Hi I had developed couple of post processing/analysis codes in earlier version of gromacs4.0.7. Now I have upgraded to gromacs4.5.1 and when I check its template file , its completely different that the earlier version. Does that mean old post-processing codes have to rewritten if I were to use new gromacs? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Amber-GS-S force field in Gromacs 4.5.1
Hello all, I noticed significant changes in my simulation results between running gromacs 4.5.1 with the included amber-gs-s force field and gromacs 4.0.7 with Eric Sorin's amber ports. I eventually figured out that the parameter files in the amberGS.ff directory are identical (up to whitespace and comments) to those of the amber99sb force field. For example: $ diff amberGS.ff/ffbonded.itp amber99sb.ff/ffbonded.itp 366c366 CK CB N* CT 4 180.00 4.18400 2; --- CK CBN* CT 4 180.00 4.18400 2; Is it possible that the parameter files got mixed up? If I understand correctly, amber-gs-s should be amber-94 without backbone dihedral potentials and without 1-4 scaling. Thanks, Lutz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul) (Justin A. Lemkul)
Message: 5 Date: Tue, 19 Oct 2010 13:06:42 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and pressurecoupling method problem (Justin A. Lemkul) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cbdd022.6020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed DeChang Li wrote: Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Umbrella sampling with temperature and pressurecoupling method problem To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4cbd9d87.6080...@vt.edu mailto:4cbd9d87.6080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but probably you need to provide more information to get a useful answer there. The Berendsen barostat suffers from the same limitations as the thermostat - the pressure distribution does not produce a true NPT ensemble. Whether the correct canonical ensemble (NPT or NVT) is important (or indispensable) for umbrella sampling? If I used the weak coupling method (Berendsen) to do the simulations, can I extract the PMF from the umbrella sampling simulations? I would think that a proper statistical mechanical ensemble would be considered indispensable for any simulation. In my mind, there is no real reason to use less accurate methods when collecting data. If your goal is a comparison of methods, or consistency with other results, sure, then you may have a reason to use algorithms that may be less than optimal. For any sensitive thermodynamic study, I would strongly argue that your potential energy surface needs to be rigorously correct. The point is this. You have to defend your choices to a skeptical audience (reviewers). This is one question that might be asked, and really should be. Methods should be scrutinized. So I would ask you this: why perform your simulations with algorithms that are not as accurate as others, when those better algorithms are accessible to you and do not harm performance in any demonstrable way? -Justin Thank you for your reply! So I will use Nose-Hoover for temperature coupling and Parrinello-Rahman for pressure coupling in the data collection. Anyway, I may do some simulations with Berendsen method to see if there is any difference in results when using the two coupling methods. -Justin -- original message -- Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = ionic bond = how to determine the direction of ionic bond dipole moment ?
Hi molecule dipole is 48.0 sum of q_i x_i For a multiple-atoms molecule, the dipole moment of a covalent bond is a vector, parallel to the bond axis, For a multiple-atoms molecule, which includes a ionic bond, how to determine the direction of ionic bond dipole moment in theory ? How does Gromacs determine the direction of ionic bond dipole moment ? Thank you Lin Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +δ -- δ- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +δ and δ-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = what is the bond length of the ionic bond in the dipole moment calculation?
Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. but what is x_i for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread among the water. What is the x_i of the ionic bond in the dipole moment calculation? Is x_i equal to the distance of the two parts of the salt-molecules (the counter ion and the rest of the molecule) even though the salt molecule has dissolved in the water? I mean, is x_i equal to the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? I mean, if Gromacs takes x_i as the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? Thank you Lin Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +ä -- ä- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +ä and ä-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/4cf32833/attachment.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
