Dear Mark, Thank you for your answer. I'm trying now with the position restraints and see what happens. However, another question came up to my mind in the mean time. I'm using GROMACS 3.3.1 (version with mapping for reverse transformation, I have been posting on it before) and for the mdrun the flag -coarse is required. From the mdrun -h help, the -coarse flag resulted to be a generic trajectory, so I assumed it was needed for the names of the atoms or something similar. However, trying to run the nvt.mdp with the original coarse grained file specified for this flag, resulted in the simulation not dying at the very first steps. I'm not sure if it will work out eventually ( the 20 ps simulations is supposed to finish in 12 hours, which is still kind of worrying despite my system being pretty big) but definitely told me that the -coarse flag might be of fundamental importance. Unfortunately I couldn't find any more detailed documentation about it. Could anyone explain to me what it does or point me to where to find the related documentation? Thank you very much Francesca
2012/3/30 Mark Abraham <mark.abra...@anu.edu.au>: > On 30/03/2012 8:39 AM, francesca vitalini wrote: >> >> Thank you Justin for your answer. I'm trying to add the position >> restraints to my protein, but I have a problem. My topology is made of >> a chain repeated twice and if I want to build the position restraints >> through genrestr from a gro file, the numeration of the atoms would >> put the 2 chains sequentially one after the other, but then the index >> would be out of bounds; > > > As genrestr -h and the manual tells you (and as was discussed on this list a > day or two ago), [position_restraints] apply to all copies of that > [moleculetype]. So use genrestr on the first molecule only and you will have > position restraints for both molecules for the price of one. > > >> if I try to generate the topology from x2top >> it has been taking more than 6 hours and hasn't finish yet. If instead >> I try to use the posre.itp built from pdb2gmx I still have the LINCS >> warnings, even after changing rlist, rcoulomb and rvdw to 1. Any ideas >> on a faster way to add my position restraints or how to solve the >> LINCS error? Thank you very much. > > > Follow the advice here > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
