[gmx-users] how to calculate g_sdf and ionic conductivity

Hello all Did anyone know how to 1) calculate g_sdf? 2) ionic conductivity? Can I have the commands for that Thanks IMA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] g_rdf and number of atoms to include

Dear users, I would like to compare interactions between molecules by using RDF. I have tried looking at glycine and water, and compare the following two interactions: 1) between the amine hydrogen atoms in glycine and the oxygen atom in water 2) between the carboxyl oxygen atoms in

Re: [gmx-users] Fatal error: 2 particles communicated to PME node 0 are more than a cell length out of the domain decomposition cell of their charge group

wuxiao wrote: > Dear GMXers, >When I perfomed a MD simulation, it always teminated after about 700 > ps with the message: > /Fatal error: 2 particles communicated to PME node 0 are more than a > cell length out of the domain decomposition cell of their charge group/ >I utilized the GROMAC

[gmx-users] Fatal error: 2 particles communicated to PME node 0 are more than a cell length out of the domain decomposition cell of their charge group

Dear GMXers, When I perfomed a MD simulation, it always teminated after about 700 ps with the message: Fatal error: 2 particles communicated to PME node 0 are more than a cell length out of the domain decomposition cell of their charge group I utilized the GROMACS-4.0.5. I have searched

Re: [gmx-users] why are the values of the LJ interaction energy negative and the values of the Coulomb interaction energy positive between two group.

Jinyao Wang wrote: > Hi gmx-users, >I have calculated the interaction energy between two group. But I find > that the values of the LJ interaction energy are negative and the values of > the Coulomb interaction energy are positive between two group. So I think the > LJ interaction is attract

[gmx-users] why are the values of the LJ interaction energy negative and the values of the Coulomb interaction energy positive between two group.

Hi gmx-users, I have calculated the interaction energy between two group. But I find that the values of the LJ interaction energy are negative and the values of the Coulomb interaction energy are positive between two group. So I think the LJ interaction is attractive and the Coulomb interacti

Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

Pablo Englebienne wrote: Thanks for confirming this, Justin. I decided not to use the user-contributed CHCl3 box because the topology is not consistent with the GROMOS atom types: the CH is united atom (although the mass is 12.01100, it should probably be 13.01900?), while in G53a5 there a

Re: [gmx-users] how to mimick explicit hydrogen bonding

ms wrote: Hi, I need to implement a FF which includes directional hydrogen bonding. It seems however, to my understanding, that Gromacs has no simple way to include an explicitly directional contribution. All I can find is that, in standard force fields, h-bond terms are implicitly described by

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Justin A. Lemkul wrote: I have also added a Perl script to the GROMACS site (the VMD page): http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD The user provides an input topology file, and a .psf file is written, which can be loaded as data for the structure in VMD. The !NBOND sect

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

I'm trying to simulate a small molecule in a chloroform box using the GROMOS G53a5 forcefield. I realized that the parameters for the solvent are present in the ffG53a5.rtp file, however I could not find a CHCl3 solvent box included in GROMACS. I did find, however, a CHCl3 solvent box equilib

Re: [gmx-users] non-standard atom names

Stefano Meliga wrote: Hello, I noticed that the command editconf -i structure.gro -o structure.pdb produce a pdb file in which some atom names are not standard. In particular the delta carbon on ILE: "CD ILE" should be "CD1 ILE"; and the oxigens of the C-terminus "O1" should be "O " "O2

Re: [gmx-users] Long Simulation Time

Chih-Ying Lin wrote: HI i was reading somewhere.. "simulation will break / terminate when the simulation is running so so long "... Did anyone read the same information? Please refer me the related information since I have no idea where I read this information. How long is lon

Re: [gmx-users] Long Simulation Time

Hi Lin, That is likely related to running with a scheduler that only allows a limited time for processes (the wall time). Under 'normal' conditions the simulation will not break due to long running times. It may break due to a full disk, which can be related to a long running time :p Cheers, Tsj

[gmx-users] Long Simulation Time

HI i was reading somewhere.. "simulation will break / terminate when the simulation is running so so long "... Did anyone read the same information? Please refer me the related information since I have no idea where I read this information. How long is long ? How to avoid this? Thank

[gmx-users] non-standard atom names

Hello, I noticed that the command editconf -i structure.gro -o structure.pdb produce a pdb file in which some atom names are not standard. In particular the delta carbon on ILE: "CD ILE" should be "CD1 ILE"; and the oxigens of the C-terminus "O1" should be "O " "O2" should be "OXT". This

Re: [gmx-users] Chloroform (CHCl3) solvent box for G53a5 force field

Pablo Englebienne wrote: Hi all, I'm trying to simulate a small molecule in a chloroform box using the GROMOS G53a5 forcefield. I realized that the parameters for the solvent are present in the ffG53a5.rtp file, however I could not find a CHCl3 solvent box included in GROMACS. I did find, h

[gmx-users] Chloroform (CHCl3) solvent box for G53a5 force field

Hi all, I'm trying to simulate a small molecule in a chloroform box using the GROMOS G53a5 forcefield. I realized that the parameters for the solvent are present in the ffG53a5.rtp file, however I could not find a CHCl3 solvent box included in GROMACS. I did find, however, a CHCl3 solvent box

[gmx-users] CMAP request

Hi Supid, We are trying to convert CHARMM force field for MTSSL (a small molecule which is used as EPR label) into gromacs format. But in CHARMM they have CMAP. I checked the gromacs mailing archive and found that there is a gromacs CVS where CMAP implementation is done. Yes, the code is in th

[gmx-users] Re: converting proper dihedrals into ryckaert-bellemans

Dear Carla, Let me suggest you the wikis at acpypi.googlecode.com. And then let me ask why amber94 and not amber99sb? And why not trying acpypi in the link above as I guess it can do pretty much what you want with much less pain? Cheers, Alan On Tue, Oct 20, 2009 at 15:55, wrote: > > Hi every

[gmx-users] Re: 1. Normal mode analysis of pure water (simon sangma)

If you are interested in the IR spectrum of water, all you need to do is a simulation of a flexible water model (not flexspc btw), save every fs, compute the dipole moment, compute the powerspectrum of that dipole moment and check for the peaks. Gerrit (tip3p_flex for instance, by skinne

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, Thanks, will be back after some trials. Ram On Tue, Oct 20, 2009 at 8:16 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the advice and suggestions, will look into the plots and >> try to run a further NPT equillibration, (here you mean equilib

[gmx-users] converting proper dihedrals into ryckaert-bellemans

Hi everyone, I'm using the amber94 force field in gromacs. I need to add topology of a new molecule for my MD simulation. I saw this line "propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet" in my ffamber94bon.itp file. So it seems that I have to convert my proper

[gmx-users] CMAP request

Dear Users, We are trying to convert CHARMM force field for MTSSL (a small molecule which is used as EPR label) into gromacs format. But in CHARMM they have CMAP. I checked the gromacs mailing archive and found that there is a gromacs CVS where CMAP implementation is done. It will be ver

Re: [gmx-users] multiple processor running of gromacs-4.0.4

Hi Mark, You are right that treating electrostatics and vdw without cutoff and use multiple processors to speed up doesn't make any sense. Using cutoff for electrostatics and vdw without using pbc and pme, the system can't run on parallel (using flag -pd doesn't work either), but works on single n

Re: [gmx-users] Error during NVT equillibration with nvt.log file

ram bio wrote: Dear Justin, Thanks for the advice and suggestions, will look into the plots and try to run a further NPT equillibration, (here you mean equilibration phase 2 ? without annealing, as in the tutorial).. Yes, normal NPT. -Justin Please let me know. Ram On Tue, Oct 20, 200

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, Thanks for the advice and suggestions, will look into the plots and try to run a further NPT equillibration, (here you mean equilibration phase 2 ? without annealing, as in the tutorial).. Please let me know. Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul wrote: > > > ram

[gmx-users] Re: AMBER force fields in gromacs program

As long as not GMX 3.x, the wikis are still valid, no matter which GMX 4.0.x you use. Alan PS: thinking twice, the wikis should even work with GMX 3.x as long as one uses the respective ffamber port. On Tue, Oct 20, 2009 at 14:38, wrote: > > dear  Alan > your suggestion is true. but I Use  gro

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

I have also added a Perl script to the GROMACS site (the VMD page): http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD The user provides an input topology file, and a .psf file is written, which can be loaded as data for the structure in VMD. The !NBOND section seems to be the most

Re: [gmx-users] Error during NVT equillibration with nvt.log file

ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average

Re: [gmx-users] AMBER force fields in gromacs program

leila karami wrote: dear Alan your suggestion is true. but I Use gromacs 4.0.3 This version difference (4.0.3 vs 4.0.5) is inconsequential for what you're doing. Otherwise, upgrade to the newest version - it has the latest features and bug fixes. -Justin ---

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct.

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What ext

[gmx-users] Normal mode analysis of pure water

Hi Berk, I want to determine the vibrational frequencies of water (close to the experimentally observed values for the three modes). And then extend the analogy for more complex systems. ___ gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] Normal mode analysis of pure water

Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What extension would the file have

Re: [gmx-users] Error during NVT equillibration with nvt.log file

ram bio wrote: Now as i would like to proceed further, please suggest me how to confirm that the simulated annealing was proper and also please let me know can i now go to npt equillibration using the output of simulated annealing as input to npt equilibration. Like you would anything els

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, Thanks. I tried to equilibrate the system in NVT ensemble without constraints, the equilibration completed, but the lipid layers moved apart, so i tried to do simulated annealing procedure mentioned in the trouble shooting section of the tutorial and here also i was able to equilibra

RE: [gmx-users] Normal mode analysis of pure water

You could get better help if you tell us what information you want to get out of this analysis. NMA gives you a harmonic description of the potential energy around a minimum of the system. For water the minimum is ice, so you would get the modes of a certain ice state. Berk Date: Tue, 20 Oct

[gmx-users] Normal mode analysis of pure water

Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P

RE: [gmx-users] Normal mode analysis of pure water

This is wasting a large amount of CPU time. Water is solid (ice) at 0 K. A plain normal mode analysis would give you the normal modes of ice. You can do a normal mode analysis of liquid water without minimization, but the standard NMA techniques will not work. Berk Date: Tue, 20 Oct 2009 18:33:4

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. Energy minimization is not the s

[gmx-users] Normal mode analysis of pure water

Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. ___ gmx-users mailin

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. You've been told twice already what the likely solution is: Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure that

[gmx-users] Normal mode analysis of pure water

Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with

[gmx-users] AMBER force fields in gromacs program

dear Alan your suggestion is true. but I Use gromacs 4.0.3 ___ 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 po

[gmx-users] how to mimick explicit hydrogen bonding

Hi, I need to implement a FF which includes directional hydrogen bonding. It seems however, to my understanding, that Gromacs has no simple way to include an explicitly directional contribution. All I can find is that, in standard force fields, h-bond terms are implicitly described by coulombic an

[gmx-users] Re: AMBER force fields in gromacs program

Please, let me suggest you acpypi.googlecode.com. There you'll find in the wikis help about installing gromacs 4.0.5 with support for ffamber. Cheers, Alan On Tue, Oct 20, 2009 at 12:55, wrote: > Hi > I want to use AMBER force fields in gromacs program for md simulation of > pr-dna interaction

[gmx-users] AMBER force fields in gromacs program

Hi I want to use AMBER force fields in gromacs program for md simulation of pr-dna interaction . I did works said in http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER *installation & Testing:* (1) Install the desired GROMACS distribution (

Re: Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Dear Nicholas, great!!! I've needed a bit time for testing but this works fine. Many thanks for that script. Thomas -- Thomas H. Schmidt, PhD student Computational Structural Biology Chair of Life Science Informatics, B-IT LIMES-Institute, University of Bonn Dahlmannstrasse 2, D-53113 Bonn, Ger

Re: [gmx-users] Gromacs version 4.0.5 - ffscan missing

Helen H. Y. Tsui wrote: Hi, I have just installed Gromacs version 4.0.5 and I've noticed one of the utility programs ffscan is missing from /bin, even though it is described in the user manual. Has anyone come across this? If so, can anyone confirm if it has been removed permanently from the

RE: [gmx-users] Erroneously documented [ settles ] directive

Hi, The manual is incorrect, settle takes one atom index. I guess this was wishfull thinking on my part. Settle does use three atoms, I don't like the current format. Also there is the hidden restriction that with domain decomposition all three atoms involved in settle should be in the same char

[gmx-users] Gromacs version 4.0.5 - ffscan missing

Hi, I have just installed Gromacs version 4.0.5 and I've noticed one of the utility programs ffscan is missing from /bin, even though it is described in the user manual. Has anyone come across this? If so, can anyone confirm if it has been removed permanently from the distribution of Grom

[gmx-users] Erroneously documented [ settles ] directive

Hi users, I note that in the manual the [ settles ] directive is said to have three atom indices (Table 5.5 in my version of the manual). In practice, and at the end of the Constraints section in the manual, only one atom index is provided. Am I misunderstanding the table, or is this a discre