> -----Ursprüngliche Nachricht----- > Von: Discussion list for GROMACS users <[email protected]> > Gesendet: 13.02.08 14:27:25 > An: Discussion list for GROMACS users <[email protected]> > Betreff: Re: [gmx-users] Strange output with Genbox
> > Jens Pohl wrote: > > Hello! > > > > I try to simulate a modified protein in a water-box. When I use genbox and > > have a look on the output-file then the water molecules are located in > > between the AA-sequence which results in an "exploding" molecule during the > > mdrun. I've done it several times from the very beginning, always getting a > > similar result (distribution of water in the AA sequence varied a bit). > > > > Input-sequence (AA): > > MGVLAI... > > > > Output after genbox: > > OMOGOOVOLOAOIOO... > > > > Commands used (copied from .bash_history): > > pdb2gmx -f 165_in.pdb -p 165 -o 165 -n 165 -i 165 -q 165_out.pdb > > > > (used ffG53a6) > > > > editconf -f 165 -o CbzE_ec.pdb -bt cubic -vol -d 1.0 > > > > genbox -cp 165_ec.pdb -cs ../Water.gro -o 165_gb.pdb -p 165_gb > > > > What is in ../Water.gro? It should be pure water. Water.gro is my renamed SPC water from the GROMACS package. > > What system are you running on? Simple Pentium IV-system with which I've done some simulations before. > > > > > Thank you very much in advance for your suggestions to solve the problem > > Jens > > Jens _____________________________________________________________________ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
