RE: [gmx-users] grompp error

Both of those errors are telling you want you need to do. In your topol_A.itp file, there are no parameters for a particular proper dihedral. So, define one. Same with the next message. And it even tells you which line the issue is on in the .itp file, so very easy to track down which bonds are

RE: [gmx-users] say something about the pull geometry of cylinder

z-axis is the length of the cylinder, parallel to the straight sides. x-y is in the plane of the circle cross section of the cylinder. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkvi

Re: [gmx-users] input the .gro and .trr file to the VMD

Best idea is to ask the vmd people, they have their own emailing list. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 28/04/2009, at 12:29 PM, "He, Yang" wrote: HI Mark, I am indeed using the coarse-graining atoms .What do you mean b

RE: [gmx-users] ffgmx:diffusion of oxygen

The issue is you don't have enough statistics to get a meaningful result. Three ways you can get more, more particles, more time, or multiply runs. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Roya

RE: [gmx-users] Error by pdb2gmx

If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.mo

RE: [gmx-users] Error by pdb2gmx

epeating units. Do you > mean I can write the rtp entry for one repeating unit and give it a > residue name. After that I need to insert this into the force field > rtp file, right? How can I do that? It seems I can not change the rtp > file. Thanks. > > On Tue, Apr 28, 2009

RE: [gmx-users] Error by pdb2gmx

Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, P

RE: [gmx-users] Test-set

Sorry, but I only performed a couple of runs using the test-set, so don't have a lot of experience, but when I did and got some fails all the information was there to help point out what the issue was. Doesn't the files in the subdirectories for each of the tests provide details of why that partic

RE: [gmx-users] RE: RE: RDF in GMX 4 (Justin)

Run input file = .tpr Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only

RE: [gmx-users] Protein-Ligand Docking?

First step, define what you mean by being "DOCKed". Second step, determine if those conditions are meet by your protein and ligand. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Pa

RE: [gmx-users] lateral stress and surface tension

http://www.gromacs.org/pipermail/gmx-users/2006-December/024953.html Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167

RE: [gmx-users] local pressure

I would recommend you have a read through the appendix in the GROMACS manual titled "Manual Pages". This has all the scripts provided with GROMACS and the manual page for them, which describes what each one does. Reading through that will go a long way to letting you know what you can and can't d

RE: [gmx-users] problem in simulation of DNA-protein complex

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_ residue_topology_database Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.

RE: [gmx-users] problem in DNA simulation

Exact same question was answered just last month . http://www.gromacs.org/pipermail/gmx-users/2009-April/040974.html Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 301

RE: [gmx-users] Protein-Ligand Docking?

Just as Mark and Justin have said, this is up to you to define this question. The reason I said that, is you were asking "how do I know if my molecule is docked to the protein?". The first step to answering that question is defining what you mean by being docked. Once you have a definition, then

RE: [gmx-users] mdp file for local pressure

The error message explicitly tells you what is wrong: "Expected 2 elements for wall_atomtype, found 0" And looking in your .mdp file ... ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpo

RE: [gmx-users] Lipids forming unsual bonds

What exactly do you mean by "unusual cross bonds"? I suspect what you are seeing is simply a visualisation artifact, with a molecule being displayed across a PBC in the viewer you are using. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceut

RE: [gmx-users] problem regarding removal of water from final simulation system.

Two ways: 1 - turn them off with the visualisation software you are using, only display the protein and lipid 2 - use editconf and the appropriate index groups Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash Un

RE: [gmx-users] pdb does not work.

Because pdb2gmx has to know what residue(s) are contained in the .pdb file, and the third column identifies the residue and as the program has told you, it is called "1". And it does not have a "1" residue on the .rtp file associated with that forcefield. Catch ya, Dr. Dallas Warren Department o

RE: [gmx-users] Fatal error

The error tells you what the problem is: Fatal error: reading tpx file (em.tpr) version 40 with version 20 program You are trying to read an em.tpr file that was generated using version 40 (as noted by the header it is GROMACS 3.3.1) using a version 20 program (as noted by the header it is

RE: [gmx-users] Lincs Warning

>Maximum force =  4.9815813e+24 on atom 169274 You should have a look at that atom, that is a large force. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

RE: [gmx-users] Segmentation Fault (Address not mapped)

> And, by the way, I have resolved the segmentation fault problem. It was > being caused by the freezing of the graphene lattice. When I removed > the > freezing, I saw the graphene structure curl upward and am thinking that > by freezing the atoms in place it was creating great forces between the

RE: [gmx-users] Segmentation Fault (Address not mapped)

> You indicate that I need to read the primary literature for the force > fields. Could you please tell me where this literature can be found? I > have searched using Google for the forcefields available for use in > GROMACS (G43b1, G43a1, G43a2, G45a3, G53a5, G53a6, gmx), but have not > found any

RE: [gmx-users] Energy Minimisation and Equilibration Problems

> Maximum force =  9.4016180e+02 on atom 31 As has already been suggested, have you looked at the atoms listed as having the maximum force to see why? >Addtionally, the structure of the solute is incorrect (all atoms are bonded to >each other). How are you visualising it? If using VMD, th

RE: [gmx-users] Suggestions for 3D-monitor/glasses for visualizing GROMACS output

Suggest you have a look and search the VMD emailing lists. These sorts of visualisation discussions come up from time to time with people sharing their experiences. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal

RE: [gmx-users] Energy Minimisation and Equilibration Problems

Have you managed to minimise a single molecule? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When t

RE: [gmx-users] Fatal Equilibration Errors

You might want to consider the parameters I developed for propylene glycol http://dx.doi.org/10.1021/mp8001667 ... might provide some guidance for you in terms of the parameterisation of ethylene glycol. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceu

RE: [gmx-users] wierd behavior of mdrun

How is it that the date and time is wrong? It is simply telling you that the simulation will be completed on Sep 16, using the time on the computer that the program is running on. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash Unive

RE: [gmx-users] how to use a new force field

Best if you don't mess with the ones that are installed. Set up your own forcefield files in a local directory and edit those, GROMACS scripts will then look in the local directory first, before going to the installed one. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharm

RE: [gmx-users] G96 bond, angle and dihedral types for unusual covalent linkages

If there isn't one in the forcefield already, then it is something that you have to parameterise yourself. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- F

RE: [gmx-users] problems with gromacs preprocessor

> Dear All, > > when I want to use grompp program > grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o > minimbrady.tpr > > I got the following error message > > Fatal error: > [ file "spc.itp", line 41 ]: > Atom index (1) in settles out of bounds (1-0) > > So I tried to m

RE: [gmx-users] Snapshots in different files

If the time frame between snapshots is not too short, you could have that as the length of each MD run, then simple extend the run to keep on going. Could be a bit inefficient. (This is how you should run MD anyway, to ensure don't lose a lot of information if the computer system you are running

RE: [gmx-users] increasing the system size

You don't really need to do anything. Atom number simply starts again. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org o

RE: [gmx-users] Load imbalance and Y size error

> No. My system is a single protein with charged ligand associated with it. But > why should box size shrink ? In solvated system it does not shrink. What > effect vacuum could possibly have on it ? Sounds very much like you have pressure coupling on. Check your .mdp file. Catch ya, Dallas Wa

RE: [gmx-users] Pressure problem: pressure is too large during MDsimulation

Plot the fluctuations of the pressure with time for the simulation. Far better way I think to get an idea of what is going on with a property than just looking at values in a log file. Especially when you are starting out. With pressure coupling, it is not unusual to have a fluctuation of a h

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

Omar's response answered that question on why they are different. In the first one you are grouping all three into one group, second is just one of the hydrogen types. The fact that the rdf you get is different indicates that all three hydrogens are not identical. Have you compared the rdf for e

RE: [gmx-users] some prolem about genbox genconf and editconf

How are you visualizing the system? Using VMD? In that case, bonds are determined by how far apart the atoms are, it guesses what the bonding is, since a .gro file (or a pdb) doesn't have any bonding information in it. So what you are seeing is simply the fact you have scaled the box, increasing

RE: [gmx-users] Docking with PyMol and using Gromacs

Coordinate files like pdb and gro aren't used by GROMACS to provide any bonding information. That is what the topology files are for. So their "presence" in your pdb isn't an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance betwee

RE: [gmx-users] Hydrated radius of ions

g_rdf ? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a ha

RE: [gmx-users] How to check for bad contacts

When you try to minimise, it will typically tell you the worst offending atoms in your system. Which you can then check visually using VMD etc and try and work out why it is an issue. Then you can adjust how the system was set up to fix the issue. Also, if you just look at the system visually

RE: [gmx-users] User results for another run

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167

RE: [gmx-users] Hydrated radius of ions

...@gromacs.org] On Behalf Of Manik Mayur Sent: Saturday, 21 November 2009 1:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Hydrated radius of ions 2009/11/20 Dallas B. Warren g_rdf ? Thanks, but while using g_rdf, when I have lots of ions, do I have to make an ndx file

RE: [gmx-users] Unexpected behavior of g_msd

trjconv Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hamme

RE: [gmx-users] spatial distribution function (SDF)

First three groups are the reference group, from which the SDF is generated, it sets the coordinate system. That means you need to have at least three "atoms" in the "molecule" you are generating the SDF from. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A

RE: [gmx-users] Re:Re: g_helixorient problem

Command lines that you use? Contents of the index files? Contents of the output files? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-bou

[gmx-users] fftw vs cmkl

Just wondering if anyone has done a comparison of GROMACS complied using fftw versus cmkl? SC tech suggested that cmkl might be a bit faster, but can't find any mention of someone making a comparison between them anywhere, searching users list and web for "cmkl" (is there may be another term us

RE: [gmx-users] fftw vs cmkl

Thanks Mark. My stats on this, GROMACS 4.0.7 compiled with gcc, run on two quad-core Xeon processors with 16GB of RAM, 100,000 atoms, PME, 200,000 steps fftw 3.2.1 - 20,027 seconds Intel cmkl - 19,792 seconds So about 1.2% faster. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Scienc

RE: [gmx-users] fftw vs cmkl

transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 12/11/2009 11:33 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fftw vs cmkl Dallas B. Warren wrote: > Thanks Mark. > > My stats on this, GROMACS 4.0.7 comp

RE: [gmx-users] splitting a trajectory

Another option is to create a new trajectory file to use in your analysis, using trjconv Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-bou

RE: [gmx-users] g_sdf and visualizing using gOpenMol

Rename it to .plt might be a good start, since that is the file extension it is meant to have (as noted in the help information for g_sdf). Also, there is an issue with the reference structure built was the script, it is not correct. Has been noted by a couple of people. Been meaning to check

RE: [gmx-users] g_sdf and visualizing using gOpenMol

t has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Dallas B. Warren Sent: Wed 12/16/2009 8:25 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf and visualizing using gOpenMol Rename it to .plt might be a good

RE: [gmx-users] g_sdf and visualizing using gOpenMol

FYI, there is a listing in bugzilla http://bugzilla.gromacs.org/show_bug.cgi?id=356 Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>-- gmx-users mailing listgmx-users@gromacs

RE: [gmx-users] Fwd: What could be wrong with rdf plot?

Wouldn't it be simpler to just exclude the intramolecular -OHs when you actually generate the RDF? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx

RE: [gmx-users] atomnumber=-12345

Might be a good idea to provide the input and output that generated the error. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 91

RE: [gmx-users] checkpoint MDRUN -cpt question

Have a read of http://www.gromacs.org/Documentation/How-tos/Extending_Simulations in particular the section down the bottom that is appropriate for the version of GROMACS you are using. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Scien

RE: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

So, what EXACTLY are you doing? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the o

RE: [gmx-users] rdf

A single methane molecule in water, it is not surprising at all that there is some noise in the rdf produced. If you want it smoother than that, you will simply having to run it for longer. The rdf is an average, insufficient data points mean it will be noisy, you cannot get around that fact. Ca

RE: [gmx-users] Assembling a good simulation starting point

Can you run that same procedure without doing anything to your protein? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167

RE: [gmx-users] energy minimization problem

Actual text input / output would be a good idea here. What is the actual output when you try to run it the second time? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dall

RE: [gmx-users] Anisotropic pressure control

Why is it that what you have run with xy rigid and z couple not correct? Fluctuating box volume is exactly what you would expect to get, and do get, with pressure coupling. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monas

RE: [gmx-users] ethanol bond types

> Thanks David. These are the parameters I added. Do you think they seem > reasonable? You might as well run a simulation yourself, it will be quickly apparent if something is very wrong. Best way to determine these things is try it and see for yourself. Catch ya, Dr. Dallas Warren Drug Deliver

RE: [gmx-users] large number of molecules

You are going to have to provide a lot more details than that if you want some help. What is "wrong results"? What is your input (copy and paste some commands in)? What is the output (copy and paste)? What makes you think the results are "wrong"? In what situations are they "right"? ... and

RE: [gmx-users] rdf problem

If you have aggregation and a small box size, then the rdf will not be able to asymptote to one. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.ed

RE: [gmx-users] density vs time

g_energy Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hamm

RE: [gmx-users] about water models

Probably already seen it, or beyond it now, but a good primer is http://www1.lsbu.ac.uk/water/models.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.mo

RE: [gmx-users] Lateral pressure profile in membrane simulations

Isn't that already present in the energy file, .edr, from the run? Simply use g_energy to extract it. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.mona

RE: [gmx-users] energy minimization in charged systems

What are the atoms that are causing the problems actually doing, where are they located etc? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +

[gmx-users] ftp Server Down?

Is it just me, or is it down at the moment? Trying to get the latest version source files. Catch ya, Dallas Warren A polar bear is a rectangular bear that has undergone a polar transformation ___ gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] Re FTP server down

Sorry seems that it was just me, or it is back up. Either way things are good now. Catch ya, Dallas Warren A polar bear is a rectangular bear that has undergone a polar transformation ___ gmx-users mailing listgmx-users@gromacs.org http://www.

Re: [gmx-users] how to get the original pdb file about CG DNA mode

Have you tried a web search? There are a number of sites that have databases of structures. Plus you could contact people that have published simulations using those molecules. What about the Protein Data Bank? Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a p

[gmx-users] Re: Benchmarks for 4.0.X

That would be right, just find it after you sent the message. Have found one now: http://www.hpcx.ac.uk/research/biochemistry/gromacs.html Catch ya, Dallas Warren Monash University <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromac

[gmx-users] Benchmarks for 4.0.X

Have these been done yet? Been trying to find some, found a few individual tests, but nothing like http://www.gromacs.org/content/view/24/37/ Catch ya, Dallas Warren Monash University <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gr

[gmx-users] RE: Benchmarks for 4.0.X

And for future reference of others, also some good data in the GROMACS 4 paper, funny enough ;-) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput., 2008, 4 (3), pp 435–447 DOI: http://dx.doi.org/10.1021/ct700301q Catch ya, Dall

[gmx-users] Parallel running of mdrun

I must be missing something here. Now we don't need to use the -np switch for grompp or mdrun, you simply specify with mpirun (4.0.3) eg mpirun -np 4 mdrun -deffnm md_01 Doing that I end up with four separate processes. Does that mean that the mdrun being used is not mpi enabled? This is

Re: [gmx-users] Parallel running of mdrun

It is one of those forehead slapping days again, d'oh Previously on this sc did not have to use the mpi on the end, but now you do. Problem solved, I think. Yep Log file now has nnodes: 2 and there is all the domain decomposition details. That is more like it :) Catch ya, Dallas Warren

RE: [gmx-users] Reidue UNK not found

May be of interest to you: http://wiki.gromacs.org/index.php/Carbon_Nanotube However, not surprising pdb2gmx failed, since UNK is not a residue specified in the residue database. pdb2gmx uses the residue name to determine what residue a particular part of your system is, then use the appropria

[gmx-users] How to get log written to file ...

Is there something that can do to force the files to be written to the disk? I am trying to work out why a simulation on a SC is not doing what it should. Problem is, only the very start of the files are present, since they are not large enough to be written, and the job reaches it's walltime (

RE: [gmx-users] How to get log written to file ...

Mark, >How the operating system manages the buffering is something you'd >usually have to talk to the OS about. "The operating system is based on SUSE SLES9 linux with an enhanced Linux 2.6 kernel and SGI ProPack4." Trawling around now to see if there is a way to force the file outputs to be

[gmx-users] Continuation of Runs and Checkpoint File Use

I just want to check that I have the new behaviour of things right. To start a simulation we have something like: grompp -f md -p KPF -c md_-1 -t md_-1 -e md_-1 -o md_0 mdrun -deffnm md_0 Now, to continue this run once it finishes, for the same length of time specified in the md.mdp file etc, w

[gmx-users] 4.0.3 goes off into la la land .... infinite loop

Alluded to this yesterday, GROMACS jobs don't finish on a SC. I have some information back from one of the admins there, they want me to post details etc so we can work out what is going on. It looks like with my input data, GROMACS going into an infinite loop in the nb_kernel100_ia64_single s

RE: [gmx-users] 4.0.3 goes off into la la land .... infinite loop

Mark, Yes, it is on ac.apac.edu.au They have also said that 4.0.2 works fine on xe.apac.edu.au (no idea what compiling settings were used, but can find out if of interest), but I have not tried it out yet. Same subroutine involved, so same issue? No idea, this sort of stuff is way over my he

RE: [gmx-users] 4.0.3 goes off into la la land .... infinite loop

I have submitted a bugzilla on this issue ... http://bugzilla.gromacs.org/show_bug.cgi?id=296 Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>__

Re: [gmx-users] How to show the created box?

There is a script in vmd to do it. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 16/02/2009, at 3:30 PM, "Chih-Ying Lin" wrote: HI after creating the box, and write it into .gro file. when i try the .gro file with VMD, but the bo

RE: [gmx-users] The difference about NPT and NVT ensemble.

> I have some questions about ensemble. Would you please tell me about NPT or > NVT ensemble? What difference about them? http://wiki.gromacs.org/index.php/Molecular_Dynamics_Simulations Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartes

[gmx-users] RE: Continuation of Runs and Checkpoint File Use

OK, well I got this wrong. If you want to extend or continue a simulation that has completed, you still have to use tpbconv. It is used to change the number of steps, then you feed that into mdrun with the checkpoint file. The only time you don't need tpbconv now is with a crashed simulation.

[gmx-users] Possible to stop mdrun changing file names when using checkpoint files?

When using checkpoint files to continue a run, mdrun overrides the output file names specified by putting ".part" before the file extension. I don't want it to do that, since I have already told it how I want the output files to be named. Is it possible to stop that happening? Catch ya, D

RE: [gmx-users] Possible to stop mdrun changing file names when usingcheckpoint files?

Justin, >> When using checkpoint files to continue a run, mdrun overrides the output >> file names specified by putting ".part" before the file extension. >> >> I don't want it to do that, since I have already told it how I want the >> output files to be named. >> >> Is it possible to stop

RE: [gmx-users] Possible to stop mdrun changing file names when usingcheckpoint files?

Chris, > One option is to avoid checkpoint files all together. I personally use > a grompp/mdrun cycle of ~2h segments that was historically done in > order to utilize the -sort -shuffle options to gromacs 3. I found it > simpler to keep on doing the exact same thing in gromacs 4, even > t

Re: [gmx-users] Possible to stop mdrun changing file names whenusingcheckpoint files?

Berk that would be handy. Option in that, could you may be have not to change the name at all and use the names specified on the command line? Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 17/02/2009, at 6:01 PM, "Berk Hess" wrote:

Re: [gmx-users] Difference between command pdb2gmx and pdb2gmx_d

The _d denotes that the command is the double precision version. Command does exactly the same things, just at double precision which may or may not make any difference to the result. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 18

RE: [gmx-users] g_rdf program

No, the molecule has not gone out the side of the box and not entered the other side. If you check the solvent on the opposite side of the box, you will notice that there is a big hole that exactly matches up with the DNA fragment that is sticking out. Use the pbc options in VMD to display neighb

RE: [gmx-users] Cross-linking of polymers

Kim, >Recently I have been focusing on cross-linking phenomenon of polymers. >As far as I understood, cross-linking include bond breaks in one polymer chain and bond occurrences among broken chains. >I guess OPLS-aa is not suitable for this purpose, and my question is this. >Is my guess correct?

RE: [gmx-users] (no subject) - fluctuations

> > Is there a way to reduce the fluctuations of the properties > calculated > > with g_energy? > Fluctuations scale as 1/sqrt(N) where N is the number of > molecules. So > the answer is yes. Depending on what you actually want to do, some smoothing of the data may be what you are after. One

RE: [gmx-users] grompp error in running simulation of lipid bilayer

Might I suggest that you refer to this webpage http://wiki.gromacs.org/index.php/Errors It would have answered both of your error questions you have posted. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University

RE: [gmx-users] How to calculate the dihedral angle variations ???

g_angle will do that fine, and with the options you used it should have done so. Possible issue that may make that fail is you failed to generate the correct angle index file for the dihedral(s) of interest. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Ph

RE: [gmx-users] density around protein

Or g_sdf Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is

RE: [gmx-users] editing .rtp files

Another to keep an eye out for, is make sure that you edited the correct .rtp file you tell pdb2gmx to use when running it. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 301

RE: [gmx-users] problem in topology file for protein+lipid bilayer system

May be have bit of a read of http://wiki.gromacs.org/index.php/Category:Force_Fields and the manual, so you can get a grip on what forcefields actually are and how you use them. I get the impression you are trying to do things here without actually understanding or even thinking about what you are

RE: [gmx-users] g_sdf

What exactly your issue with using g_sdf? You need to supple a trajectory, index, and topology. Index contains the three reference atoms for the molecule, plus the atom you are calculating the sdf to. Selection of the correct grid size and binwidth is required to get something that looks as you

RE: [gmx-users] g_sdf

That is entirely up to you. The forth paragraph in the help explains how the three atoms in the index are used to generate the coordinate system. Best idea with anything like this, have a play, see what comes out, see if it is what you want, then try again. Play with it like that will also help

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