Re: [gmx-users] Strange error from my simulation

And if you're at it, also change your temperature coupling...(check the archives). Tsjerk On 5/21/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Stéphane Téletchéa wrote: > While switching from NVT to NPT, i'm crashing my simulation. > > The error message seen is (repeated 10 times, then mdrun abo

Re: [gmx-users] readxtc can not get coordinates without jump?

Hi Zhongqiao Hu, Actually, the first procedure will give the wrong results. With option -b the frames up to that point will be skipped. So the first frame read, at t(b), will have the jumps removed against the reference structure given. But in 10 ns, a lot may have happened, making the reference

Re: [gmx-users] Strategy for chaining jobs using different mdp parameters (long)

Stéphane Téletchéa wrote: Dear colleagues, I've done many chained simulations up to now but i'm encoutering problems and i'm skeptical about some choices i made before. In order to clear this up, i'd like you to share your experience, so that'll answer my needs and be a good template for the

Re: [gmx-users] Strange error from my simulation

Stéphane Téletchéa wrote: While switching from NVT to NPT, i'm crashing my simulation. The error message seen is (repeated 10 times, then mdrun aborts): # Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20 -1.59647e+20 -1.59647e+20 Correcting invalid box: old box (3x3): ol

Re: [gmx-users] fatal error grompp !

Philippe Reymond wrote: Dear Gromacs Users, I just installed Gromacs on my windows machine (with a gromacs especially for Windows XPdownloaded) from your website. Everything seemed to go fine with the installation and there is no problem when I execute pdb2gmx, editconf and genbox. But, when

[gmx-users] fatal error grompp !

Dear Gromacs Users, I just installed Gromacs on my windows machine (with a gromacs especially for Windows XPdownloaded) from your website. Everything seemed to go fine with the installation and there is no problem when I execute pdb2gmx, editconf and genbox. But, when I execute grompp, I get t

Re: [gmx-users] Strange error from my simulation

Stéphane Téletchéa wrote: While switching from NVT to NPT, i'm crashing my simulation. The error message seen is (repeated 10 times, then mdrun aborts): # Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20 -1.59647e+20 -1.59647e+20 Correcting invalid box: old box (3x3): ol

Re: [gmx-users] gromacs-antechamber-gaff

Francesco, At any event, one should be aware (if I understand correctly) that to convert from Amber to Gromacs with the alchemistry script below, one should have also the Amber code installed. Should it work at all with Amber 9, instead of the Amber 7 suggested. Yes, this works with AMBER 7, 8

Re: [gmx-users] gromacs-antechamber-gaff

Sorry to have been the spark for troubles. At any event, one should be aware (if I understand correctly) that to convert from Amber to Gromacs with the alchemistry script below, one should have also the Amber code installed. Should it work at all with Amber 9, instead of the Amber 7 suggested. I

[gmx-users] Strange error from my simulation

While switching from NVT to NPT, i'm crashing my simulation. The error message seen is (repeated 10 times, then mdrun aborts): # Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20 -1.59647e+20 -1.59647e+20 Correcting invalid box: old box (3x3): old box[0]={-9.82630e+20,

[gmx-users] Strategy for chaining jobs using different mdp parameters (long)

Dear colleagues, I've done many chained simulations up to now but i'm encoutering problems and i'm skeptical about some choices i made before. In order to clear this up, i'd like you to share your experience, so that'll answer my needs and be a good template for the upcoming wiki. I want (an

Re: [gmx-users] gromacs-antechamber-gaff

David, On 5/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Francesco Pietra wrote: > Planning to use gromacs aided by antechamber/gaff for > my recurrent need of new bonded parameters, and having > noticed that antechamber's tutorial refers to Sybyl > and Gaussian, my question: > > Is it

Re: [gmx-users] Testing Gromacs

Kedar Potdar a écrit : Hi all, I could build Gromacs successfully on Linux system and now I would like to test it. So is there a way to test Gromacs? Does the Gromacs package come with basic test suites? I couldn't find anything pertaining to testing on the Gromacs' site. Help in this r

Re: [gmx-users] REMD log files

N-J.M. Macaluso wrote: Hi, Thanks for your previous responses to my questions on REMD. I have a general question about understanding REMD in gromacs. Can someone break down how to read the .log file? For instance, one of the main goals I have is to graph the time evolution of temperature e

Re: [gmx-users] Polarizability

Hi Jones, Charge-on-spring model is another name for shell model. Here's what's written in the introduction of the paper: [...]in the charge-on-spring (or Drude-oscillator or shell) model, an additional point charge is attached to a polarizable center that can adapt its position to the electric fi

Re: [gmx-users] Polarizability

Hi Patrick. Just got this paper here, thanks for the indication. This may sound like a dumb question, but: am I wrong, or the "shell model" and the "charge on a spring model" differ only by the fact that the VdW interation is also "floating aroung" in the "shell model" but not in the "charge on

[gmx-users] REMD log files

Hi, Thanks for your previous responses to my questions on REMD. I have a general question about understanding REMD in gromacs. Can someone break down how to read the .log file? For instance, one of the main goals I have is to graph the time evolution of temperature exchange for a specific

Re: [gmx-users] Polarizability

Hi, there's a very recent paper of the GROMOS team, where they evaluate the free energy of polarization (with the 'Charge-on-Spring' model): http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html Their code is already working, but under the GROMOS software... Ciao, Patrick Jon

Re: [gmx-users] Re: Calculate individual force between each atom pair

Hi, On May 20, 2007, at 11:50 PM, WU Yanbin wrote: Thanks for the suggestions. I have traced the calling sequence from do_force() to calculate LJ forces: do_force() -->force() -->do_nonbonded(). But in do_nonbonded() function of nonbonded.c file, if for general processor, it should ha