Re: [gmx-users] basic units: acceleration conflict (revision)

Let me summarize the conflict in this example: The acceleration to be applied corresponds to 2x10^12 meter/(second squared) (in words: two times ten to twelve) which means in vacuum that water molecule may gain two times ten to twelve meter/second velocity at every second (e.g. for dilute cas

Re: [gmx-users] ngmx,dssp not working

Dear gmx-users, I have installed the gromacs 3.3.3 on a dual core HP workstation with Ubuntu platform. All the programs are properly installed and working except ngmx and dssp. However there is a difference, ngmx is not installed as I donot see the link in /usr/local/bin along with the oth

Re: [gmx-users] Covalent bonds breaking formation

Probably, you shold use qm/mm hybrid methods to do it Look at the following page, this is the best tutorial I found for hybrid calculations in gromacs (though didn't tried actually to do it) http://www.dddc.ac.cn/embo04/practicals/qmmm/introduction.html 2008/7/3, Sagittarius <[EMAIL PROTECTED

Re: [gmx-users] compilation problem with mopac in gromacs 3.3.3 and x86_64 machine

2008/7/8 Abu Naser <[EMAIL PROTECTED]>: > > Hi Gerrit, > > I am having problem during compilation as : > > /mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH': > qm_mopac.c:(.text+0x2fc): undefined reference to `domop_' > ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac':