[gmx-users] g_rdf in fedora core 5

I compiled and installed gromacs 3.3.1 in Fedora Core 5 using gcc 4.1.0, now,when I want to use it ,it always displays "Reading frame0 time 0.000". Does anyone have the same problem with me? Is there any method to solve the problem? Thanks very much in advance. ___

Re: [gmx-users] Problems using grompp and amber force field

our .top file so we can have a look > at it > > Tom > > --On 08 May 2007 10:53 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote: > > > root wrote: > >> Dear GROMACS user: > >> > >> Erik and Tom thanks by the comments, too. Sorry, I read the

Re: [gmx-users] Problems using grompp and amber force field

e AMBER > family of force fields and can be ignored. > << > > Did you try doing that? > > Good luck! > > /Erik > > 7 maj 2007 kl. 22.29 skrev root: > > Hi, >I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then >

Re: [gmx-users] Problems using grompp and amber force field

this. Thanks in advance root wrote: De: David van der Spoel <[EMAIL PROTECTED]> Responder a: Discussion list for GROMACS users Para: Discussion list for GROMACS users Asunto

[gmx-users] Problems using grompp and amber force field

Dear GROMACS user: David and Mark, thanks by our comments, suggestions and questions. If our response is confused, please require us copies of output files (or fragment). The procedure to simulate the DNA dodecamer was: 1) We generate the DNA topology and coordinates in gromacs format (with the

[gmx-users] Document about file input format to GROMACS program?

Dear GROMACS user: We downloaded the AMBER-03* potential parameters files (ffamber_v3.3.1-doc.tar.gz) linked with the page http://folding.stanford.edu/ffamber/index.html#validation. We tried to simulate the Dickerson dodecamer using the 3.3.1 gromacs version. Our simulation crash when we run the g

[gmx-users] small molecules simulation

Hello everyone,today I tried to simulate several small molecules, however I failed. The process is like this: I got DRG.gro and DRG.itp files from the PRODRG website, and used the command "genbox" to obtain a random listed conf.gro of 33 phenol molecules. Then I include "ffgmx" and " DRG.ITP” to g