[gmx-users] REMD demuxing

Hello everyone, I'm trying to find a better way of demuxing REMD runs, I wrote a python script to do this but it is very slow because it relies on system calls to trjconv in order to read/write frames. I checked the documentation and mailing lists, it seems that this should be possible using "t

[gmx-users] ci value

Dear Gromacs users, I am trying to run a steep minimization for a protein in a system containing 15% TFE and 85% water. When I executed mdrun I obtained the following message: Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ] Please report this to the mailing list

Re: [gmx-users] tau_p

> Hi, > > I wonder what is the point of posting this kind of messages to the list: > >>Yeah, that :-) >>Mark The point of my email was to acknowledge the error I made in confusing tau_p for ref_p, which Tserk was gently correcting. > Moreover, Mark, this issue is rather well explained in Berendse

Re: [gmx-users] Error in .top when running grompp for final product MD

> Dear gromacs users, > > > > I am running MD for a protein with 212 amino acid residues. > > When I run grompp (grompp -f pn_md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top > - > o pn_md.tpr ) for the final product MD, I receive the following error > message. > > I properly included sol and ion in the

[gmx-users] tau_p

Hi, I wonder what is the point of posting this kind of messages to the list: Yeah, that :-) Mark Moreover, Mark, this issue is rather well explained in Berendsen's paper of the 80`s (!!) and in the manual (p 24). Regards. Pedro. ___ gmx-users mail

Re: [gmx-users] dihedral

Dear Prasad, I did not follow the whole issue, but you could also exploit the fep code for rotating around a bond. Just define in state A the dihedral potential such that it has its minimum at, say, 30 deg, and in state B, the dihedral has its minimum at, say, 150 deg. Then you do a slow growth sim

Re: [gmx-users] gromacs 4 release date?

Chris Neale wrote: Any projection date for a release? Of particular interest to me is whether it is very likely to come out before Jan 1 2008. I hope we can release it before summer, but it depends on what we decide to put in it besides the new parallelization. Since it will be a major upgrad