RE: [gmx-users] Error in using gromacs for MD simulation

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war

[gmx-users] RE: ask about SDF

things gradually more complex. That way you can work out if you are using the script incorrectly or what you expected to see is actually incorrect. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade

RE: [gmx-users] Error in using gromacs for MD simulation

, used the wrong, old file in a new step etc. Many ways you may have gone wrong. Is it 1 SOL atom or 1 SOL molecule? Be very careful with your terminology with things like that, can seem the same to someone starting out, but they are very different. Catch ya, Dr. Dallas Warren Medicinal

RE: [gmx-users] Box of water

Easiest solution can think of, make box that is of sufficient size the when filled contains 846 waters, fill with waters, use editconf to scale the box size to that which you require, run EM to get the waters back to the dimensions they should be. Catch ya, Dr. Dallas Warren Medicinal

RE: [gmx-users] Error in using gromacs for MD simulation

on Windows, yes GROMACS can be installed on that OS, see the website for details on how to do that. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903

[gmx-users] RE: Re: CO2/gromos53a5

with that FF. Otherwise you are going to have to spend a fair amount of time sorting it out yourself. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3

[gmx-users] RE: Regarding errors

have observed see http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry If that is not the reason, there are a couple of others that I have noticed being mentioned on the emailing list. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

RE: [gmx-users] Proper 1-octanol box preparation

appears to be at least 3 times too large for the number of molecules you have inserted. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] the radius of dry core

Via the methylene - COM RDF. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own

RE: [gmx-users] the radius of dry core

RDF = probability function Methylene density (number in the box (Nt) divided by the box volume), multiplied by probability (RDF) and shell volume (r+dr) calculates number of methylenes (Nm) within a given shell. Fraction = Nm/Nt Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action

[gmx-users] RE: Cut off problem

. These have particular values as defined by the forcefield, and you need to use those. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] Regarding error

Have you incorrectly changed the numbers in the topology, the difference in the number is 8, so it appears your coordinate file contains 8 more atoms than the topology. You will have to work out how that is. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical

[gmx-users] mdrun -j still functional?

for a number of versions, developers aren't working on it, so now it is broken? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

[gmx-users] RE: mdrun -j still functional?

in which it is working) or update the code yourself so that it is working again. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] a residue move in extremely large scale in MD

What information has told you that you have large scale movement? Where did that information come from, how was it generated? Have you watch the trajectory of this simulation to see how the residue actually moves? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute

RE: [gmx-users] a residue move in extremely large scale in MD

and it sinks in better too. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every

RE: [gmx-users] a residue move in extremely large scale in MD

. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail

RE: [gmx-users] a residue move in extremely large scale in MD

You are missing a major conceptual principle of MD here. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Read manual, section 3.2 Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal

RE: [gmx-users] Protein-POPC bilayer

what is reasonable and you get severe box distortion and failure. Will be saying a little on that in an upcoming paper Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war

RE: [gmx-users] BAR / g_bar problems

Trivial question, how do the TI results compare? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool

RE: [gmx-users] Holes in the solvent!

My suggestion would be that this is a periodic boundary condition artifact, what you are seeing is the holes in the solvent due to a chain protruding out of the opposite face of the simulation box. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences

RE: [gmx-users] query regarding mk_angndx

the system/molecule that has the same parameters as the script will group them together into one if you are not careful. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3

RE: [gmx-users] combine two gro files

Why is it that you want to combine the two coordinate files? md.gro is the coordinates of the system at the end of 20ns. md_extend.gro is the coordinates of the system at the end of 22ns. So combining them will not make much sense. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash

RE: [gmx-users] How to include a small organic molecule

There is a spelling mistake on the above line, forcefield.itp #include popc.itp #include ligand.itp . [molecules] ;compound #mols Protein_chain_A 1 POPC 276 ligand 1 SOL 8748 Catch ya, Dr. Dallas

RE: [gmx-users] polymer duplicate atoms

The residue number is not incrementing in your coordinate file (it stays as 1), so it thinks it is all the same residue. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war

RE: [gmx-users] Re: polymer duplicate atoms

to where you want to be. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem

RE: [gmx-users] Re: polymer duplicate atoms

Have you done it with polymer chain of length 1, one FRE, with the end methyl groups capping it off, FBG and FEN? Does that work? Sounds bit like the RTP entry is not set up correctly. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash

RE: [gmx-users] Re: polymer duplicate atoms

like this ... [ Fbg ] [ bonds ] C4+C1 C4H11 C4H12 C4H13 [ Fen ] [ bonds ] C1-C4 C1H11 C1H12 C1H13 Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381

RE: [gmx-users] Re: polymer duplicate atoms

with the polymer monomer unit, otherwise you wont be able to automatically cap it. Another option is to have a Fbg and Fen that includes a capped monomer unit, rather than just the methyl group. That may be a better way to go about it. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash

RE: [gmx-users] construct the long polymer chain

For people to provide solutions, you will need to show at least what happens when you use more than six, i.e. the errors you get, structures / topologies that are not correct etc. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University

RE: [gmx-users] Radial density calculation

Just calculate the radial distribution function from particle-to-particle. You can then integrate that probability to get a mass density at a given radius, using the average overall system density. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences

RE: [gmx-users] plots in gromacs

(with the appropriate filtering options). Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own

[gmx-users] RE: keeping water (entirely) out of the bilayer core

require. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins

RE: [gmx-users] equilibration of the simulated systems

That really depends on what property it is that you are interested in observing. You need to observe the dynamics of the property of interest, see over what time frames it changes, then ensure that you simulation time is enough to cover it equilibrating or changing. Catch ya, Dr. Dallas

RE: [gmx-users] Fwd: Rycaert-Bellemans function

to remove pairs. If it comes from the OPLS FFs, then you need to leave the pairs in. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] Large number of solvent molecules

molecules, then you will need to make the simulation cell smaller. Whether that is possible or not depends on what you are looking to observe, how big the molecule you are solvating is etc. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University

RE: [gmx-users] Regarding Table Extension

. table-extension = 20 ; (nm) !IMPORTANT! Set this so that rvdw + table-extension equals half of the box's longest diagonal. Are you aware of the situation to which that sample .mdp file is used? Is that situation applicable for what you are doing? Catch ya, Dr. Dallas Warren Medicinal Chemistry

RE: [gmx-users] Re: PBC - Protein - ligand

at which the ligand is interacting. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you

[gmx-users] RE: Questionable van der waals volumes from g_sas

Sorry, ignore my last post, only just realised you had set your probe to 0 radius. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

[gmx-users] RE: Questionable van der waals volumes from g_sas

Jake, Wont the volume be a function of the probe radius that is used? And hence, if it is too big to fit through the ring, the volume will be larger than if the chain was straight? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences

RE: [gmx-users] density

Last bit here, that is probably done using a RDF, which is a probability function, which you can then convert into a number of atoms in each shell. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade

RE: [gmx-users] The time correlation functions for the orientation of the C-H

Check Chapter 8 and Appendix D of the manual. You can use g_analyze to generate an autocorrelation function for any data / property that you can feed it, if there isn't something built into a particular script. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute

RE: [gmx-users] NVT simulation

If you are just getting a feel for these things, use the -v switch with mdrun, this makes it verbose, and prints out lots of messages letting you know how much longer it will be etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences

RE: [gmx-users] density

I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf –h”, method is outlined there and I suspect there are a number of discussions on it within the emailing list archive that you should search. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

RE: [gmx-users] UNK not found

http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3

RE: [gmx-users] Error when try obtain protein energies instead of system energies

at the step where you generated those two files, that is likely to be where the issue is. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] glutamic acid protonation

pKa = 4.1 Protonation state of the acid group depends on the pH that you are performing the simulation at. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war

RE: [gmx-users] Regarding Simulation of KALP-15 in DPPC

What exactly did you try? What was the result? Actually copy and paste the commands and output. Saying it didn't work is insufficient detail for anyone to help you. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University

RE: [gmx-users] how to know the pH of a solution

to 1. That will require a very large system to get a statistically significant number of protons in there. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu

RE: [gmx-users] Ice Crystal Structure

http://www.google.com.au/search?q=ice+crystal+coordinate+fileie=utf-8oe=utf-8aq=trls=org.mozilla:en-US:officialclient=firefox-a Second listed item contains (or leads you to where you can find them) pdb files for ice Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

RE: [gmx-users] how to understand this sentence

Have you run g_energy on the .edr file and extracted the box dimensions during the run to see what has been happening to them? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010

RE: [gmx-users] Re: Protein ligand simulation

One file you used had the coordinates in angstroms, the other in nanometers. You cannot have numbers with different units in the same coordinate file. Which is what you did. Hence why they are not in the locations you assumed they were. Catch ya, Dr. Dallas Warren Medicinal Chemistry

RE: [gmx-users] File input/output error pdb2gmx command

Though this looked familiar: http://lists.gromacs.org/pipermail/gmx-users/2011-November/066557.html What are the permissions for the file? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville

RE: [gmx-users] dihedral format in top file?

Section 5.3.3 of the manual. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own

RE: [gmx-users] coordinate number aroud the first shell

1 - number of atoms divided by size of the box. 2 - manually or via a script. I have a script set up within Sigma Plot that I use for mine, but can be done in any other spreadsheet and programming language too. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute

RE: [gmx-users] Help with g_density

What is your interpretation? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own

RE: [gmx-users] pressure profiles

It will be saved in the .edr file. Use g_energy to extract the data you are interested in. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903

RE: [gmx-users] another question about performance

Recheck the units for that last number …. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only

RE: [gmx-users] g_rdf

An RDF is normalised to the density for the entire box, so you should simply be using that. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903

RE: [gmx-users] g_rdf

d(r) = (N/V)*g(r) Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer

RE: [gmx-users] g_rdf and lipid bilayer hydration

with VMD using the 2 button). Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own

RE: [gmx-users] Triple bond

http://lists.gromacs.org/pipermail/gmx-users/2009-July/043186.html Plus there are several others http://www.gromacs.org/Support/Mailing_Lists/Search?q=triple+bond Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University

RE: [gmx-users] air-water interface

Search the literature and see what others have done to do exactly this. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] interface

What does it look like when you visualise the coordinate file? That is how you can answer that question, as we certainly can't. And as you will soon find out, you cannot have a single interface in a simulation box, you have to have two. Catch ya, Dr. Dallas Warren Medicinal Chemistry

RE: [gmx-users] analysis pdb file

) from the trajectory file using trjconv for the appropriate times interested in. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] quick question about restart

I use the second option there on all my simulations, using a script. Simulations are done in 10ns blocks, at the completion of that the pbs script submits the next job. Have found this way much less hassle, better computer utilisation etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry

RE: [gmx-users] dihedral distributions

of reaching some equilibrium. Catch ya, 3 - you will have to look at the type of dihedral it is and the potential function it creates, then check to see if the observed distribution is consistent with that. Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical

[gmx-users] g_sdf - and g_spatial

of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash

RE: [gmx-users] Cluster analysis

You would be best off using an RDF of particular atoms/functional groups to the waters. You can then integrate that and get the number of waters within a given distance. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash

RE: [gmx-users] on gromacs force field

are interested, or do some work validating that it is actually appropriate. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] About the function of -v' in mdrun

Slang for “it says a lot”, being verbose (which is what –v means), lots of information printed out. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3

RE: [gmx-users] a question related to the extending of md

What .edr files are listed in the directory? Seems simply a case that the first section of the trajectory energy file has a separate file name to the last, i.e. the results weren't appended to the initial .edr file. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

RE: [gmx-users] a question related to the extending of md

Also, it is easy to join the two .edr files together, using eneconv However, it is probably better for you to simply start again and get the simulation to complete in one go. It should not take long to do. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute

RE: [gmx-users] Re: how to g_select bound water molecules

For future reference of others that may struggle with g_select, it would be a very good idea for you to put on the emailing list how you achieved it. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade

RE: [gmx-users] regarding micelle and its analysis

, then pass each group to g_gyrate separately to get the radius for each micelle. From what you have written you have calculated the radius of gyration of all of the surfactant molecules within your simulation, which is more than likely not what you want. Catch ya, Dr. Dallas Warren Medicinal

RE: [gmx-users] afm simulation

Don't add water and don't use pressure coupling. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When

RE: [gmx-users] liquid/liquid

Easiest way is probably set up the appropriate sized box for molecule 2, randomly distributed molecule 3 in appropriate number through it (genbox), then solvate that box with molecule 2, then combine that box with solvated box containing molecule 1. Catch ya, Dr. Dallas Warren Medicinal

RE: [gmx-users] Umbrella sampling of phosphate ion binding

You have been provided there with the reference in which the parameters for the molecule were derived. Read it! And determine yourself if it is applicable or not to what you are doing and the forcefield you are using. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

[gmx-users] Umbrella sampling of phosphate ion binding

/Documentation/Terminology/Force_Fields#Usage and the first point at http://www.gromacs.org/Documentation/How-tos/Parameterization Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war

RE: [gmx-users] Re: Gromacs error

be able to sort out what the issue actually is, seems to be something to do with how files are handled with Fedora, and then the correct course of action. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal

RE: [gmx-users] Re: Increase in charge after adding the ligand

those numbers. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every

RE: [gmx-users] Re: Increase in charge after adding the ligand

Go back through your procedure, repeating it again, step by step. Take note of number of atoms, charges etc as you go. And answer the other questions I put to you previously. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash

RE: [gmx-users] xvg plotting

Any graphing program will do, the .xvg file is a text data file, so you can import it into Excel, Sigma Plot, xmgrace, gnuplot etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010

RE: [gmx-users] X and Y dimensions in nanometers

What was the issue you had with g_gyrate? As that is the best tool for this job. Do you have pbc issues? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu

RE: [gmx-users] phase transition in MD simulation

to do that. It could simply be a poor model to use for showing phase behaviour. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] radial distribution function

be an easier way to do this, but this would make it easy to see). Appears it may be something real, so just check the coordinate file and see where they are actually coming from. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash

RE: [gmx-users] radial distribution function

in Angstroms and GROMACS in nm. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own

RE: [gmx-users] g_msd: Not enough points for fitting (0). Can not determine the diffusion constant

and -beginfit -endfit are not consistent with each other. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When

RE: [gmx-users] g_analyze doubt

, the command you want to run is g_analyze -f data.xvg -ac autocorr.xvg as you have a data file with time (x) and variable (y) data and you want the autocorrelation function of the variable data. Have you tried that command? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute

RE: [gmx-users] VACF

, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins

RE: [gmx-users] Pressure estimation from NVT

Have you looked at the data from which you calculated the pressure average from? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] Pressure estimation from NVT

My suggestion was to actually physically look at the data you are using to calculate the average. Make a graph of pressure versus time. Something as simple as actually looking at the data can tell you a lot, rather than just pulling the average from somewhere. Catch ya, Dr. Dallas Warren

RE: [gmx-users] Re: simulation of protein/water and phosphate ion

What is actually blowing up? The protein or the phosphate ions? Do the phosphate ions run OK by themselves in water? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war

RE: [gmx-users] Re: simulation of protein/water and phosphate ion

And where are these waters? Close to the phosphate ions? You really need to be asking more questions, looking at the trajectory file / frames when it blows up, and determining what is actually going on by yourself. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

RE: [gmx-users] NVT equilibration of Ethanol in OPLSAA.

Sounds very much like you have an insufficient number of molecules in the box to fill it up. If you look at the pressure data for the simulation, I suspect you will find that it is negative, the box wants to decrease in volume. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action

[gmx-users] RE: NVT EQUILIBRATION

. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble

RE: [gmx-users] NVT Equilibration

smaller box, which may be an issue. But, closer you are to the correct starting point when you build the box the better. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war

RE: [gmx-users] Regarding Density

until it reaches the appropriate density. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only

RE: [gmx-users] Ligand scattered out of the protein

PBC issue? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] Implicit solvent problems

Did you look at atom 2073? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own

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