[gmx-users] How to set constant pulling force in pull.ppa with AFM option?

Dear all,  Would anybody tell me how to do it? I don't understand clearly what's meaning of those parameters in pull.ppa with AFM otion? Thanks a lot! Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.___ gmx-users mailing lis

[gmx-users] Constructing New Metal-Containing Topologies in OPLS

Hello gmx'ers, I've been developing new residue topologies for the OPLS FF. These are backbone-bound Cu-complexes, where the metal is coordinated directly to a deprotonated amide N-atom, such as is observed at the N-terminal end of serum albumin. I’m getting reasonable results, but unfortunately r

Re: [gmx-users] N-terminal and C-terminal modifications

List User wrote: What is the best approach to handle N and C-terminal modifications (e.g. formylation, chemical modification)? Is it better to define custom residue types or to adjust the termini database? Thanks in advance for your advice. I would suggest custom residue types and/or termini,

RE: [gmx-users] Fatal Error: moleculetype K is redefined

--- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype K is redefined --- I believe this error is due to your forcefield files, the .itp files that y

[gmx-users] Fatal Error: moleculetype K is redefined

Hi,While trying to setup a membrane inserted protein simulation I get this following error while running grompp command. % grompp -v -f em.mdp -c br1.pdb -p example.top -o br_emin.tpr Generated 1369 of the 2211 non-bonded parameter combinationsExcluding 3 bonded neighbours for Protein_A 1 Cleaning

[gmx-users] Re: request

sina wrote: Dear developers, I am a member of Computational Chemistry research group at university of Tehran. In one of our recent projects, we needed software for executing our MD calculations. In these respect, we chose GROMACS software because of its great utilities in MD simulations. We’v

[gmx-users] Details of force field

  Hi, Can somebody tell me where can i get the details about the G43a1 force field or can someone send me the paper by van Gunsteren 1996 on the same? Thanx, Arunima ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailm