Re: [gmx-users] glutathionylation and SS bonds formation in GMX

Hi Luca, As Marc mentioned, they have to be recognized as one molecule (-merge). In addition, it is not just that the distance has to be less than that given in the specbond.dat file, it has to fall within a 10% range aruond that distance. Cheers, Tsjerk On 1/12/07, Marc F. Lensink <[EMAIL PRO

Re: [gmx-users] infinitive force acting on atom during minimization

Hi Joern, Did you first perform an energy minimization in vacuum? The values you get indicate severe problems with your starting structure. By the way, for such a system you don't want to use a cubic box. It's an utter waste of resources. You're better off with a rhombic dodecahedron, or you can

Re: [gmx-users] Segmentation error (core dump)

> Dear gmx-users, > > I installed the gromacs-3.3.1 on Cygwin and no problems occured, but when > I execute the commands such as g_angle,pdb2gmx, all commands gave the > message: Segmentation fault (core dumped) at the end. Anybody have met > this problem ever? How to resolve it? > Thanks for any a

Re: [gmx-users] Has the forces for virtual sites in the trr filebeen reditributed?

Yes they have. You can also see that the force on the virtual site is zero. Got it! Thanks a lot _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/

Re: [gmx-users] Essential Dynamics Sampling (EDS) MD

I've rerun everything from scratch following Bert's input. The numbers seemed all right, but the runs still failed. Then I tried using just a subset of the eigenvectors, which has worked so far (i.e. it's running for about 1ns). Bert and Lars - thanks a lot for your help, Ran. Bert de Groot wrote