Re: [gmx-users] Coordination number

Sir Thank you for the reply. The higher graph is also broader and I thought should then give a higher coordination number. Does gromacs use the box density? does it not use 4*pi*r2*g(r) for calculating rdf (thats what I read in a paper where the authors have used gromacs for simulation and analyse

[gmx-users] g_hydorder error

Dear all, I am using following command in gromacs version 4.5.5: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1.xpm file2.xpm But getting following error: Internal error in pbc_dx, set_pbc has not been called In my mdp file, I have set pbc to xyz I have searched the archive and found that simila

Re: [gmx-users] g_hydorder error

On 8/26/13 8:27 AM, Nidhi Katyal wrote: Dear all, I am using following command in gromacs version 4.5.5: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1.xpm file2.xpm But getting following error: Internal error in pbc_dx, set_pbc has not been called In my mdp file, I have set pbc to xyz I hav

Re: [gmx-users] Gromacs 4.6.3 Installation Issues,

probably u do not have CUDA. If you are not really interested in performing simulations using GPU, you can set -DGMX_GPU=off during cmake On Sat, Aug 24, 2013 at 12:15 PM, No One wrote: > hi, > > i'm having difficulties installing gromacs by creating static links to the > libraries for fftw3. >

[gmx-users] error with g_dist

Hello all, I am trying to find the distance between 2 centres of mass using g_dist. I use the command: g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx but i get the error: Fatal error: Molecule in topology has atom numbers below and above natoms (1707). You are probably trying to use

Re: [gmx-users] error with g_dist

On 8/26/13 4:05 PM, chinnu657 wrote: Hello all, I am trying to find the distance between 2 centres of mass using g_dist. I use the command: g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx but i get the error: Fatal error: Molecule in topology has atom numbers below and above nato

[gmx-users] Re: error with g_dist

I'm basically trying to see how the distance between the ligand and protein changes with time using their centres of mass and the only way I've come across is by using g_dist. I'm pasting the contents from the terminal after the doing a gmxcheck on the md_0_1.xtc file which is my .xtc file from th

Re: [gmx-users] Re: error with g_dist

On 8/26/13 4:39 PM, chinnu657 wrote: I'm basically trying to see how the distance between the ligand and protein changes with time using their centres of mass and the only way I've come across is by using g_dist. I'm pasting the contents from the terminal after the doing a gmxcheck on the md_0

[gmx-users] Re: error with g_dist

Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the protein and one being the ligand (JZ4) screenshot.png sorry, you may have to zoom in. I'm not sure how to snip on linux still. Chinnu -- View this me

Re: [gmx-users] Re: error with g_dist

On 8/26/13 4:58 PM, chinnu657 wrote: Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the protein and one being the ligand (JZ4) screenshot.png sorry, you may have to zoom in. I'm not sure how to snip on

[gmx-users] Re: error with g_dist

1 and 13 Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010742.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

Re: [gmx-users] Re: error with g_dist

On 8/26/13 5:05 PM, chinnu657 wrote: 1 and 13 I don't see how this error would be possible unless you accidentally chose group 22. Choosing 1 and 13 should be perfectly viable. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow De

[gmx-users] Re: error with g_dist

No, I chose 1 and 13. I just tried again, but the error is still the same.. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010744.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx

Re: [gmx-users] Re: error with g_dist

On 8/26/13 5:35 PM, chinnu657 wrote: No, I chose 1 and 13. I just tried again, but the error is still the same.. Send me your .tpr file, a coordinate file (.pdb or .gro) of the system, and your index file off-list and I will look into it. -Justin -- ==

[gmx-users] Re: error with g_dist

I've copy, pasted the text after selection: eading file md_0_1.tpr, VERSION 4.5.5 (single precision) Group 0 ( System) has 33037 elements Group 1 (Protein) has 1693 elements Group 2 ( Protein-H) has 1301 elements Group 3 (C-alpha) has 163 elements G

[gmx-users] Re: error with g_dist

md_0_1.tpr - production simulation .tpr file 3HTB_clean.pdb - .pdb file after removing hz4 coordinates JZ4.pdb

Re: [gmx-users] Re: error with g_dist

On 8/26/13 5:47 PM, chinnu657 wrote: md_0_1.tpr - production simulation .tpr file 3HTB_clean.pdb - .pdb file after removing hz4 coordinates JZ4.pdb

[gmx-users] Re: error with g_dist

Mine still gives me the same error. I don't quite understand why since it's giving u the right output. Im using the same version as you too. If you do not mind, could you give me the .xvg file? So that I can use it as a result. Simultaneously, I'll see what I can do to solve the problem with your

Re: [gmx-users] Re: error with g_dist

On 8/26/13 6:03 PM, chinnu657 wrote: Mine still gives me the same error. I don't quite understand why since it's giving u the right output. Im using the same version as you too. My guess would be that your installation is buggy, usually the fault of a bad/outdated compiler. Without signifi

[gmx-users] Re: error with g_dist

ok that's ok then. this was the school system. so I can't really reinstall it. I'll try and use a cluster. Hopefully, it works. thanks a lot Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010751.html Sent from the GROMACS Users Forum mai

[gmx-users] Re: error with g_dist

I won't be submitting these though. just letting you know. I just need to explain how all of these can be achieved. Just clarifying. But thank you for all the help you've provided. It's been very valuable help. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-wi

RE: [gmx-users] Coordination number

I don't know how g_rdf script uses any density to calculate the cumulative number RDF, I have always calculated the RDF then done the integration myself to determine the coordination number. You need to look at the data you have in front of you, work out the density yourself, integrate yourself