[gmx-users] Re: helical parameters for DNA

Hello, you can use for example Curves (Nucleic Acids Research, 2009, Vol. 37, No. 17 5917-5929) or 3DNA (http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html) to calculate them from any trajectory, I did but never used gromacs for this, I don't know if it is possible. Hope this helps, Best Attilio

Re: [gmx-users] nsgrid error

> Attilio Vargiu wrote: >> Hi All, >> I'm simulating a drug-DNA complex in water, with the AMBER force field >> and >> running GROMACS in parallel on 8 processors. >> After ~100 ps, I get the error here below: >> >> - >> Program mdrun

[gmx-users] nsgrid error

Hi All, I'm simulating a drug-DNA complex in water, with the AMBER force field and running GROMACS in parallel on 8 processors. After ~100 ps, I get the error here below: - Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighbo

[gmx-users] calculate number of contacts

Hi All I want to calculate the number of contacts between a small molecule and a oligonucleotide from a MD run. I read in the manual that in the itp file is possible, setting 2 for the combination rule within the section [ defaults ], to give sigma and epsilon instead of c6 and c12 LJ parameters. I