Re: [gmx-users] Cytochrom C

Have you try www.pdb.org? http://www.pdb.org/pdb/explore/explore.do?structureId=3cyt Nuno On Thu, Jan 5, 2012 at 4:40 PM, Dariush Mohammadyani < d.mohammady...@gmail.com> wrote: > > Hi all, > > Has anybody made initial configuration for Cytochrom C? Can it be shared > with me? > > Thanks, > Dar

Re: [gmx-users] problem in finding gromos53a6.ff

gromos53a6.ff. Nuno Azoia On Fri, Jan 20, 2012 at 10:31 AM, Anushree Tripathi wrote: > I am using gromacs 4.5.3 version and I am trying to follow the tutorials. > For > starting I am following the *KALP15 in DPPC* > > tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justi

Re: [gmx-users] Using shell script to analyze the results

There is a more direct way. In the script just use g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm < wrote: > Create a file named input.g_rms. write the group number in this file. In > your shell script after command line write executed in shell the file input.g_rms having group number will be read. >

Re: [gmx-users] Using double ndx as input ?

You can not use different index files. You must use different groups in the same index. Merge the 2 ndx into one single file. Cheers Nuno Azoia On Fri, Feb 15, 2013 at 1:58 PM, 라지브간디 wrote: > How do i use two different ndx file ( which has few residues) as a input > to calculate between

Re: [gmx-users] numbering after 99999SOL

I'm guessing that you are using .gro file format. That's a limitation of the file format. See http://manual.gromacs.org/online/gro.html If you really need different residue number for each residue, use .g96 file format instead. Cheers Nuno Azoia On Tue, May 14, 2013 at 3:08 PM, gro

Re: [gmx-users] numbering after 99999SOL

I'm sorry. I get confused with residue number and atom number. For the analysis and other Gromacs tools, you will need a index file. Gromacs do not use residue number or atom number, so it's not a problem to have two or more residues with the same residue number. Nuno -- gmx-users mailing list

[gmx-users] Pressure very high with chloroform and gromacs-4.5.5

Hello! I found something very strange while making a CHCl3 box using gromacs-4.5.5. A look the mailing list, the manual and some release notes for gromacs-4.5 and I couldn't found the answer for my problem. It's possible that I'm doing something wrong, but I can not find what, so I'm describe my p

Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5

in small droplets), and that's why I found the system behavior very strange. I will follow your suggestion concerning nsttcouple and nstpcouple and the other initial conditions. Nuno Azoia On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham wrote: > On 12/10/2011 2:22 AM, Nuno Azo

Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5

le to divide the system into small, but interdependent systems. On Wed, Oct 12, 2011 at 12:26 PM, Mark Abraham wrote: > On 12/10/2011 8:04 PM, Nuno Azoia wrote: >> >> Thank you Mark for your answer! >> >> I agree with you when you say that the high pressure is not it

Re: [gmx-users] Stimulation stopped at 2ns

n the .mdp file but grompp did not change the .tpr file, if already present. Cheers Nuno Azoia > > > it is nsteps=500. I don't see any stdout and stderr files. >> >> > These are standard streams, not files. Some qu

Re: [gmx-users] lipid_posre.itp file

Hi Nitu You cab use the Gromacs tool genrest. Nuno On Tue, 2009-05-12 at 12:28 +0530, nitu sharma wrote: > Dear all > > I need lipid_posre.itp file can anyone suggest me > from where I can find it ?or If I have to make it by my own then > please let me know how can I make it

Re: [gmx-users] pdb2gmx does not recognize residues

residue number. It should work. But again, check the pdb file format, or just use some software to write the pdb for you. You can use Pymol, for example, and then just rename the residues. Nuno Azoia On Fri, 2009-05-15 at 10:11 +0200, Rolf Erwin Isele-Holder wrote: > Hello everybody, > > I

Re: [gmx-users] installation

o use /usr/local/gromacs/bin/pdb2gmx. Replace "/usr/local/gromacs" with the directory where you install gromacs. If you didn't choose anything it probably is /usr/local/gromacs. I hope this can help Nuno Azoia On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote: > hi,I

Re: [gmx-users] mdrun seems stuck

Take a look to your .log file. Gromacs writes everything there. Nuno Azoia On Tue, 2009-06-02 at 10:45 +0100, Stefano Meliga wrote: > Hello, > > I'd like to run a position restrained MD of a protein in water with > 3000 (protein) + 4 (SOL) atoms. > > I preprocess the

Re: [gmx-users] installation

On Wed, 2009-06-03 at 00:42 +1000, Mark Abraham wrote: > Nuno Azoia wrote: > > Hello! > > > > Just like Manik Mayur suggested, the problem should be the links: > > Making links may fix the problem of finding executables if that link > location is already in yo

Re: [gmx-users] do_dssp

Hi Leila! Can I add just one more note? The file dssp, that you put in the right place, has the permissions to be executed? Nuno Azoia On Wed, 2010-01-06 at 15:35 +0330, leila karami wrote: > dear Rasoul > > I put executable DSSP in /usr/local/bin and gromacs is > in /usr/l

Re: [gmx-users] MPI ERROR while installing GMX4.0.7

quot;/your/directory" with the correct path in your system. I hope this will help. Nuno Azoia On Fri, 2010-01-15 at 12:30 +0530, Chandan Choudhury wrote: > Hello gmx-users !! > > I am trying to install gromacs 4.0.7 double precision with mpi. I > downloaded openmpi-1.4. and ins

Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

Erik Lindahl wrote: MSVC should be able to compile it, but you'll have to create the makefiles/build environment yourself. Alternatively, the easy route is to install cygwin (or get a mac ;-) or keep your computer and run it under Linux :D (I can not resist) Nuno Azoia Cheers, Eri

[gmx-users] Problems with grompp and posre.itp in gromacs 4.0

t; #include "protein_C.itp" In every of this itp files I have something like this ; Include Position restraint file #ifdef POSRES #include "posre_A.itp" #endif Thank you in advance for your help. Nuno Azoia -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em A

[gmx-users] Problems with grompp and posre.itp in gromacs 4.0

nditions, but this don't make any sense to me. Can anyone help with this? What do I have to do to solve this problem? Tank you Nuno Azoia -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Textil Universidade do Minho Campus de Azurém 4800-0

Re: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0

re.itp file I've created) makes no sense because by that way I was calling each posre_*.itp file twice: once in the .top file and the other in posre.itp file. Grommp was reading the posre.itp file first, without any reference to any molecule, and it just don't work. Thank you very much! Nuno

RE: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0

lti-chain system, having no posre.itp file? Nuno Azoia > > From the file names it seems that the files are non-standard > and made of modified by hand. > So maybe you somehow modified a file with posre.itp in it? > > Berk > > > > Date: Wed, 5 Nov 2008 10:11:03 -05

Re: [gmx-users] x2top

Just a very silly question: having a pdb file, why don you use pdb2gmx instead. It will give you a topology file and you can select any force field, not only those accepted in x2top. In the x2top man page there is a Known Problem with ffG43a1.n2t. Once again, maybe this is silly, but I think i

Re: [gmx-users] x2top

Sorry about that. I realize now that my question is really very stupid. If you try to use pdb2gmx you will have a erro message just like "atom type not found". I have this problem, write first and think a little bit more after. Nuno Azoia wrote: Just a very silly question: having

[gmx-users] Selecting force field for simulation in vacuum

ions in vaccum? If I search on the mailing list I get the advice of using G43b1. Can anyone help me on this. And just another small thing. Maybe it would be good to remove the reference to G43b1 on the pdb2gmx man page. Thank you in advance. Nuno Azoia -- Nuno Gonçalo Azoia Lopes Labora

RE: [gmx-users] Selecting force field for simulation in vacuum

d but I can't downloaded (Phys. Rev. Lett. 96, 147801 (2006)). Ok, now it's up to me. I'm thankful for all the help. I have some good reading ahead of me. Nuno Azoia On Thu, 2008-12-04 at 13:36 +0100, Berk Hess wrote: > Hi, > > It depends on what you mean with vacuum simu

Re: [gmx-users] query about random velocity generation

Hi Sangeeta I don't know if it's the best option, but in a situation like yours I just used gen_seed = -1 (minus 1). By this way every time you do a simulation the gen_seed number will be different, because the program generates a random number. I hope this will help. Nuno Azo

Re: [gmx-users] (no subject)

temperature of your system to chage. Nuno Azoia On Thu, 2009-02-12 at 17:32 +0530, sharada wrote: > Dear gromacs-users, > > I am heating a peptidein methanol from 0K - 300K. The simulated > annealing protocol is given in the md.mdp file shown below: > >

Re: [gmx-users] editconf and genbox using method

Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options Nuno Azoia On Mon, 2009-03-09 at 12:23

Re: [gmx-users] editconf and genbox using method

Exactly. In my simulations with octahedron box I encounter the same problem. I just transform it in pdb to use it with pymol, that's all. But I have to use the same kind of options Justin use. Nuno Azoia On Mon, 2009-03-09 at 07:10 -0400, Justin A. Lemkul wrote: > > Mark Ab

Re: [gmx-users] Re: warning mesgs

k you have to repeat the last pdb2gmx command in order to create the .gro file, something like pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.*gro* -inter –merge -ignh (the same command you have written but with different output file) Nuno Azoia rams rams wrote: Dear Justin,

Re: [gmx-users] simulate Gas Phase system

Chih-Ying Lin wrote: Hi to simulate the gas phase system, before running MD on the gas phase system I have to use the "editconf" command. But, I DO NOT use "genbox" command. I'm new to Gromacs, but I think that if you do that you will running simulation in vacuo. Maybe it a good approximat

Re: [gmx-users] mdrun -nice integer

y and with nice value = 19 it's very low priority. Check your system processes to check the nice values of each one. Nuno Azoia Chih-Ying Lin wrote: Hi for the mdrun command, what does "-nice integer" mean? I have read the manual, but still have

Re: [gmx-users] box size

Chih-Ying Lin wrote: Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? These values represents the real dimensions of the box 2. for the editconf command, editconf -d Distance_between_the_solute_and_the

Re: [gmx-users] box size

Chih-Ying Lin wrote: Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? These values represents the real dimensions of the box 2. for the editconf command, editconf -d Distance_between_the_solute_and_the

Re: [gmx-users] do_dssp

pcmbi. So, before try do_dssp I create a soft link "dssp" to the binary dsspcmbi. I've created the link in the same directory (/usr/local/bin), and everything is just work fine. Nuno Azoia Justin A. Lemkul wrote: minnale wrote: Thanks for the reply Justin I tried like thi

Re: [gmx-users] coarse grain dynamics

quot; you need to do some "all atoms" simulation, not coarse grain. Nuno Azoia On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: > Dear Gromacs Users, > > I have done coarse grain simulation for 2 peptides in bilayer for > 1000ns, and now i would like to know the hydrogen bond