Re: [gmx-users] Martini Cg-model can not be downloaded!

I had the same problem with Internet explorer. Try Firefox! Andrei On Tue, Feb 10, 2009 at 9:41 AM, xi zhao zhaoxiitc2...@yahoo.com.cn wrote: well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model

Re: [gmx-users] Martini Cg-model can not be downloaded!

It's caused by the IE. 2009/2/10 xi zhao zhaoxiitc2...@yahoo.com.cn well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Parameters.html, the cg model parameters can

[gmx-users] Re: Martini Cg-model can not be downloaded!

Which browser do you us? I had the same problem with Internet explorer. Try Firefox! Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

Re: [gmx-users] Martini Cg-model can not be downloaded!

On Feb 10, 2009, at 9:54 AM, weixin wrote: It's caused by the IE. what is IE ? 2009/2/10 xi zhao zhaoxiitc2...@yahoo.com.cn well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model parameters

[gmx-users] (no subject)

Respectable Mark/Berk/David I am trying to study diffusion of oxygen in water at a constant pressure of 1 bar. My system contains 2 oxygen molecules in 110 water molecules of the box size 1.5 nm I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run mdp file.   When I run the

[gmx-users] energy and coordinates at different times

Dear All, I am starting some simulations and would like to write out some coordinates more frequently than others, is this currently possible. Below is how I envisaged using the commands, however it seems that I don't quite understand. Is something like this possible and how do I implement this?

[gmx-users] Magic Number Error in XTC file

Hello, I am trying to joing different .xtc fragments of a gromacs trajectory using trjcat (Gromacs 4.0.2 version). trjcat_sp -f file1.xtc file2.xtc -o join1_2.xtc I get the following error: (...) Reading frame 1 time 22202.002Summary of files and start times used:

Re: [gmx-users] Magic Number Error in XTC file

Rebeca García Fandiño wrote: mailto:gmx-users@gromacs.org Hello, I am trying to joing different .xtc fragments of a gromacs trajectory using trjcat (Gromacs 4.0.2 version). trjcat_sp -f file1.xtc file2.xtc -o join1_2.xtc I get the following error: (...) Reading frame 1 time

Re: [gmx-users] (no subject)

Sunil Thapa wrote: Respectable Mark/Berk/David I am trying to study diffusion of oxygen in water at a constant pressure of 1 bar. My system contains 2 oxygen molecules in 110 water molecules of the box size 1.5 nm I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run mdp

[gmx-users] Formating PDB Files

Hello, I am experimenting with formatting pdb files using pdb2gmx. Currently I am downloading ligand files from RCSB.ORG. These are non-protein pdb files. When I look at their residues, instead of having a standard residue, they use their pdb id as the residue id. pdb2gmx does not like this

Re: [gmx-users] Formating PDB Files

Jack Shultz wrote: Hello, I am experimenting with formatting pdb files using pdb2gmx. Currently I am downloading ligand files from RCSB.ORG. These are non-protein pdb files. When I look at their residues, instead of having a standard residue, they use their pdb id as the residue id. pdb2gmx

[gmx-users] P-N vector orientation

Dear Xavier Periole I am a GROMACS user, presently working with DMPC  bilayer. I want to calculate the orientation of the head groups P-N vector. From gmx-users,  I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair

[gmx-users] Virial from non-bonded forces

Hi,   I have two main issues:   1. In Appendix B of the GROMACS user manual, there is a discussion of the calculation of the virial. The top of the second page of the appendix (just before B.1.2) states, In a triclinic system there are 27 possible images of i, My question is: In this case,

Re: [gmx-users] shake for water

Berk, Ah, now we are talking about something completely different. Settle gets me at least 1e-10. Are you sure your problem is in the water and not in the molecule with LINCS? For LINCS you will need to change lincs_order to at least 8 and lincs_iter to something probably something around

Re: [gmx-users] P-N vector orientation

Hi Anindita, This program I had a long time ago and unfortunately it has been lost during my movings. I think you should try to contact: Andrei. Gurtovenko Biophysics and Soft Matter Group Laboratory of Physics Helsinki University of Technology P.O.Box 1100 FIN-02015 HUT Finland Tel.:

[gmx-users] Re: Martini Cg-model can not be downloaded!

I encountered the same problem when I using IE or other Browsers based on IE. You could try ViewPage tools integrated in Maxthon broswer,all the addresses of file that linked in the webpage can be extracted.I have extracted them in the webpage you provided,you can download them directly:

[gmx-users] question about .trr file

Dear all, at present, when I'm doing a simulation (with Gromacs 3.3.3), I'm keeping both .trr and .xtc files, the first one in case of a continuation of the simulation, and the second one for analysis. As I saw in the manual and in the gmx-users list, the .trr file is essential for an EXACT

Re: [gmx-users] question about .trr file

Anna Marabotti wrote: Dear all, at present, when I'm doing a simulation (with Gromacs 3.3.3), I'm keeping both .trr and .xtc files, the first one in case of a continuation of the simulation, and the second one for analysis. As I saw in the manual and in the gmx-users list, the .trr file is

Re: [gmx-users] Virial from non-bonded forces

Omololu Akin-Ojo wrote: Hi, I have two main issues: 1. In Appendix B of the GROMACS user manual, there is a discussion of the calculation of the virial. The top of the second page of the appendix (just before B.1.2) states, In a triclinic system there are 27 possible images of i, My

Re: [gmx-users] shake for water

David Mobley wrote: Berk, Ah, now we are talking about something completely different. Settle gets me at least 1e-10. Are you sure your problem is in the water and not in the molecule with LINCS? For LINCS you will need to change lincs_order to at least 8 and lincs_iter to something probably

[gmx-users] funny zero-step mdrun results in 4.0.3

All, I'm trying to run a zero-step mdrun in 4.0.3 (basically just to evaluate the energy of a specific configuration). I've done this test in 3.3.x and am trying to check if 4.0.3 gives the same energies. I'm also comparing against another simulation package. To this end, I have my starting

[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

Re: [gmx-users] Gromacs 4.0 Benchmarks

Robert Fenwick wrote: Hi, I wanted to run one of the gromacs 4.0 benchmarks on a new cluster that we have and also wanted to see the affect of this 4 fs time step. If it would not be too much trouble would it be possible for the setups of either the PLINCS paper or the GROMACS 4.0 paper to be

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

Dallas B. Warren wrote: 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. If this is ac.apac.edu.au, then I had problems with various GROMACSen 4

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

Re: [gmx-users] question about .trr file

Anna Marabotti wrote: Dear all, at present, when I'm doing a simulation (with Gromacs 3.3.3), I'm keeping both .trr and .xtc files, the first one in case of a continuation of the simulation, and the second one for analysis. As I saw in the manual and in the gmx-users list, the .trr file is

Re: [gmx-users] funny zero-step mdrun results in 4.0.3

David Mobley wrote: All, I'm trying to run a zero-step mdrun in 4.0.3 (basically just to evaluate the energy of a specific configuration). I've done this test in 3.3.x and am trying to check if 4.0.3 gives the same energies. I'm also comparing against another simulation package. To this end, I

[gmx-users] DOPC + Cholesterol topology and forcefield files

Hi, Does anyone know where I can get a well-equilibrated DOPC + Cholesterol bilayer, with cholesterol anywhere between 30-50 mole % and total number of lipids somewhere around 100 ? Thanks, Hari ___ gmx-users mailing list