Re: [gmx-users] hydrogen on N (OPLS_241), zero sigma and epsilon

n N (OPLS_241), zero sigma and epsilon st wrote: Hi There, I am very thankful to your help always. I am working with a system containing a carbon nanotube, a poly ether (charge -1), and a Na+ in spc water. I use OPLSAA for the poly ether, water and Na+. The poly ether is connected via a peptide b

[gmx-users] hydrogen on N (OPLS_241), zero sigma and epsilon

Hi There, I am very thankful to your help always. I am working with a system containing a carbon nanotube, a poly ether (charge -1), and a Na+ in spc water. I use OPLSAA for the poly ether, water and Na+. The poly ether is connected via a peptide bond (-CO-NH-), and I use OPLS_241 for the hydr

Re: [gmx-users] mdrun running without simulating new steps

5e+03 -- From: "Justin A. Lemkul" Sent: Tuesday, September 01, 2009 4:35 PM To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] mdrun running without simulating new st

[gmx-users] mdrun running without simulating new steps

Hi, I run a two-molecule system with mdrun_d in a water box (~1 water molecules.) The program looks running properly (no errors nor warnnings) However the program seems stop outputting files (because the output file size stop increases) after about 5min. The mdrun_d interface looks normal wi

[gmx-users] problem installing gromacs

Hi There, I have some problems installing gromacs on the linux server. fftw installed with no error, but when I install gromacs, I got the following error: * /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wal