Re: [gmx-users] orthorhobmic box??

Hie Tsjerk, Thanks a lot for your reply. I have another doubt! What is the difference between the "system size" & "box vectors"? system size : 7.280 6.135 6.445 (nm) center : 3.180 2.380 3.130 (nm) box vectors : 6.360 4.760 6.260 (nm) box angles : 90.00 90.00

Re: [gmx-users] orthorhobmic box??

Hie Tsjerk, thanks a lot for your reply. I have another doubt! What is the difference between the "system size" & "box vectors"? system size : 7.280 6.135 6.445 (nm) center : 3.180 2.380 3.130 (nm) box vectors : 6.360 4.760 6.260 (nm) box angles : 90.00 90.00

Re: [gmx-users] How to keep intact hdrogen coordinates from a PDB file

Nicolas SAPAY wrote: Hello everybody, I want to convert a .pdb file into a .gro using pdb2gmx but I have some troubles with hydrogen coordinates : they are all modified by pdb2gmx during the process. Actually, all hydrogens have been added previously (with CHARMM), as well as the N- and C-termin

Re: [gmx-users] finding diffusivity at desired region in a simulation box

Thank you very much for your suggestion, Sir. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTE

[gmx-users] How to keep intact hdrogen coordinates from a PDB file

Hello everybody, I want to convert a .pdb file into a .gro using pdb2gmx but I have some troubles with hydrogen coordinates : they are all modified by pdb2gmx during the process. Actually, all hydrogens have been added previously (with CHARMM), as well as the N- and C-terminal patches. When I give

Re: [gmx-users] time estimation script

Martin Höfling wrote: Am Dienstag, 27. Februar 2007 schrieb David van der Spoel: but it says at the bottom of the md.log file how many ns/day you will get. ah ok, I know what you mean: Setting up a short run ~200 steps or so and then parsing md.log file. That's a good idea. My solution would

Re: [gmx-users] Advices needed!

When starting a new thread, please delete the text of an old message that isn't pertinent. Not only will this prevent spurious data being sent to hundreds of people, but later when people go to search the archives of this list, they won't come up with erroneous results. Triguero, Luciano O wro

RE: [gmx-users] finding diffusivity at desired region in a simulation box

Best bet probably, with what is already available, is to create an index group that is in the location, then measure the diffusion of those. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade

Re: [gmx-users] how to extract frames

Hello Tanos ! check trjconv help, trjconv -h -dt time 0 Only write frame when t MOD dt = first time (ps) So you may try: trjconv -s $input.tpr -f $input.xtc -o output.pdb -dt 10 On 2/27/07, Tanos França <[EMAIL PROTECTED]> wrote: Hi folks, I can not remember how to pro

[gmx-users] how to extract frames

Hi folks, I can not remember how to procedure to extract frames from the .trr file after the dynamics simulation. I have performed a MD simulation of 1 ns with a step 0,5 fs and I would like to know how to extract frames in .pdb files at each 10 ps. Could someone help me with this matter

[gmx-users] Chimera GROMACS support

Hi, The latest snapshot release of UCSF Chimera (versions 1.2348-50) now has explicit support for GROMACS trajectories. It requires .tpr and .trr files as input. If you try it out and run into problems or have suggestions, let me know. The Chimera home page is here: http://www.c

Re: [gmx-users] orthorhobmic box??

Hi Priyanka, You also have to set the -angles between the vectors. Otherwise editconf assumes a rectangular box. Cheers, Tsjerk On 2/27/07, priyanka srivastava <[EMAIL PROTECTED]> wrote: Dear All, Is it correct to use the following command for generating an orthorhombic box? editconf -box

[gmx-users] orthorhobmic box??

Dear All, Is it correct to use the following command for generating an orthorhombic box? editconf -box x y z -f test.gro -o final.gro test.gro has (0 0 0) as box dimension whereas final.gro has (x y z) Eagerly waiting for response, Priyanka S.

[gmx-users] Advices needed!

Hello everyone, Does anyone in the list know how to overcome this problem? Error message after 2010 iter in mdrun simulation Warning: 1-4 interaction between 278 and 281 at distance 1.863 which is larger than the 1-4 table

Re: [gmx-users] restarting a sorted shuffled trajectory

My problem was that i used the wrong .top and .gro (the sorted and shuffled one) file with the sorted, shuffled trr. The discrepancy came from the pre-processed .tpr (since one need to provide the .top and .gro linked into the processed .tpr tpr). Problem solved, run done (still need a lot of

[gmx-users] Question about g_cluster groups

Hi all, I'm using g_cluster with the -dm option to provide a pre-calculated RMSD-matrix of my trajectory. I therefore assume than g_cluster won't need to do any RMSD calculations, since it can take all the distance information it needs from the xpm matrix. Nevertheless g_cluster asks me to provi

[gmx-users] finding diffusivity at desired region in a simulation box

Hi all, I am trying to study the properties of Argon by NVT simulation. The configuration file of Ar which I generated fills the half of simulation box (cuboid) with Ar atoms and rests nothing. After running the simulation I found that some regions of cubiod were highly packed with Ar compare

Re: [gmx-users] g_traj with xtc_grps ... all coordinates zero

When starting a new topic, please start a new email with a new subject line. Not only does this maximize the chance that people who know the answer to your problem will read about your problem, but you use everybody's time more efficiently. ravi kant wrote: I am trying to study the properties

Re: [gmx-users] segmentation fault

Hi Priya, What is the rationale for decreasing box dimensions, if it explodes? First of all, does your peptide fit in a box with dimensions 0.9 nm? And what about your cut-off length? I would think that with such a small box, your peptide overlaps with its own periodic images, giving a good recip

Re: [gmx-users] time estimation script

Martin Höfling a écrit : Am Dienstag, 27. Februar 2007 schrieb David van der Spoel: but it says at the bottom of the md.log file how many ns/day you will get. ah ok, I know what you mean: Setting up a short run ~200 steps or so and then parsing md.log file. That's a good idea. My solution wo

[gmx-users] segmentation fault

Dear All I am facing a problem in gromacsafter running MD in water for a a linear peptide steps i did... 1. created a box of dimensions 0.9nm , added water molecules 2. did energy minimization 3. Position rest MD for 20ns 4. Production MD for 1ns But it ends with segmentat

[gmx-users] problems with nsgrid

Dear gmx users I'm simulating a system with 128 POPC, 5000 water (SPC) and 1 peptide with dummy hydrogens (option -vsite hydrogens in pdb2gmx) and 4fs of time step to reproduce the bilayer assembling, starting from molecules randomly placed inside the box. The system has been minimized and an

Re: [gmx-users] time estimation script

Am Dienstag, 27. Februar 2007 schrieb Stéphane Téletchéa: Merci bien! It looks very verbose. I'll try to implement sth similar for 3.3 in my python scripts. Cheers Martin -- Nur, weil man vor sich eine CPU hat, muß man das Denken nicht einstellen. [Marcus Stoegbauer, dang, 23.11.2003]

Re: [gmx-users] time estimation script

Am Dienstag, 27. Februar 2007 schrieb David van der Spoel: > but it says at the bottom of the md.log file how many ns/day you will get. ah ok, I know what you mean: Setting up a short run ~200 steps or so and then parsing md.log file. That's a good idea. My solution would have been killing mdru

Re: [gmx-users] restarting a sorted shuffled trajectory

[EMAIL PROTECTED] a écrit : Thanks a lot for you all, i realise i haven't posted i found the solution of my problem, as pointed by Yang Ye (thanks). My problem was that i used the wrong .top and .gro (the sorted and shuffled one) file with the sorted, shuffled trr. The discrepancy came from t

Re: [gmx-users] time estimation script

Martin Höfling a écrit : Am Dienstag, 27. Februar 2007 schrieb David van der Spoel: mdrun -v Yep, I know that :-) But maybe someone has already implemented a script parsing the output of a test mdrun? Something like what i've attached ? I used this script to parse the benchmark results

Re: [gmx-users] time estimation script

Martin Höfling wrote: Am Dienstag, 27. Februar 2007 schrieb David van der Spoel: mdrun -v Yep, I know that :-) But maybe someone has already implemented a script parsing the output of a test mdrun? Cheers Martin ___ gmx-users mailing list

Re: [gmx-users] time estimation script

Am Dienstag, 27. Februar 2007 schrieb David van der Spoel: > mdrun -v Yep, I know that :-) But maybe someone has already implemented a script parsing the output of a test mdrun? Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] time estimation script

Martin Höfling wrote: Hi there, has anybody here already written a time estimatior script to find out how many ps/day one can calculate on a specific machine? Or did i miss a gromacs feature to do this? Cheers Martin ___ gmx-users mailing l

[gmx-users] time estimation script

Hi there, has anybody here already written a time estimatior script to find out how many ps/day one can calculate on a specific machine? Or did i miss a gromacs feature to do this? Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.

Re: [gmx-users] g_traj with xtc_grps ... all coordinates zero

Hi all, I am trying to study the properties of Argon by NVT simulation. The configuration file of Ar which I generated fills the half of simulation box (cuboid) with Ar atoms and rests nothing. After running the simulation I found that some regions of cubiod were highly packed with Ar compared t