答复: [gmx-users] about ending basepairs in DNA simulation

in DNA simulation On 6/04/2010 11:51 PM, Wu Rongqin wrote: > Dear all, > > I am doing simulation on a short B-DNA which containing 11 basepairs. My > interest is on the middle basepair in the sequence. During the > simulation, I found severe distortion on the two basepairs at b

[gmx-users] about ending basepairs in DNA simulation

Title: about ending basepairs in DNA simulation Dear all, I am doing simulation on a short B-DNA which containing 11 basepairs. My interest is on the middle basepair in the sequence. During the simulation, I found severe distortion on the two basepairs at both ends, for example, the dihedral

[gmx-users] how to get averaged coordinates for a residue in a time interval?

Title: how to get averaged coordinates for a residue in a time interval? Dear all, How to get the averaged coordinates for a short time range say, 10 ps? which utility should be used? r. q. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

[gmx-users] how to get angle-time data?

Title: how to get angle-time data? Dear all, As we can get the distance variation with time steps in gromacs, but how can we get an angle (defined by 3 noncolinear atoms) variation with time? Regards R.Q. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

[gmx-users] averaged pressure not consistent with set value

Title: averaged pressure not consistent with set value Dear all, I performed NVT md to my system and found that T is ok. However, from there I continued to NPT and found that after 100ps, the veraged Pressure is -4.0 bar, far away from 1 bar I set. Is this because 100ps is not enough for pres

答复: [gmx-users] compile problem on Cen tos X86_64 with gcc44 and fftw2

problem on Centos X86_64 with gcc44 and fftw2 Wu Rongqin wrote: > Dear all users, > > I compiled the program likes this: > > a, fftw3 >   ./configure --enable-float make   make install. All sounds ok > b, gromacs4.0.5 >   ./configure --with-fft=fftw3  make make install. Al

[gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2

Title: compile problem on Centos X86_64 with gcc44 and fftw2 Dear all users, I compiled the program likes this: a, fftw3   ./configure --enable-float make   make install. All sounds ok b, gromacs4.0.5   ./configure --with-fft=fftw3  make make install. All sound ok. However when I copy gmxt