Re: [gmx-users] Problem with trjconv centering after fitting

[EMAIL PROTECTED] wrote: Starting from a rhombic dodecahedron xtc file, trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless, a_fit_cent.xtc shows

Re: [gmx-users] The water model with tip5p in gromos96

主月 ：） wrote: Hi everyone: I found that in tip5p.itp, there is a note tell user to use tip5p model with opls force field. But what i really want to use is the gromos96. How can i include tip5p model? copy the vanderwaals parameters for the TIP5P oxygen to the ffG43a1nb.itp file. Thanks

[gmx-users] The water model with tip5p in gromos96

Hi everyone: I found that in tip5p.itp, there is a note tell user to use tip5p model with opls force field.   But what i really want to use is the gromos96. How can i include tip5p model?   Thanks a lot *Ji QingInstitute of Chemistry

[gmx-users] Problem with trjconv centering after fitting

Starting from a rhombic dodecahedron xtc file, trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless, a_fit_cent.xtc shows overlapping atoms and regio

Re: [gmx-users] free energy: annihilation

David Mobley wrote: Yuguang reminds me of something else... I just did a bunch of hydration free energy calculations for a large set of small molecules. These tend to be pretty accurate for stuff that is mostly nonpolar, but the larger the charges are, the bigger the deviation from experiment can

Re: [gmx-users] more than one settle type?

Samantha Kaye wrote: Dear gmx-users, I am trying to set up a restrained run of my protein and water simulation on gmx3.3 I ran the enmin stage on the same machine using the same version of gromacs. The restrained run keeps crashing with this error: Fatal error: More than one settle type (2831

Re: [gmx-users] Making two defaults sections compatible

Steven Kirk wrote: Hello, I'm using a macromolecule with the OPLS-AA force field, solvated with SSWM4-DP polarizable water (many thanks to DvS for this). The .itp file for the polarizable water has a [defaults] line that looks like: [ defaults ] LJ Geometric whereas when the OPLS-AA fo

[gmx-users] Making two defaults sections compatible

Hello, I'm using a macromolecule with the OPLS-AA force field, solvated with SSWM4-DP polarizable water (many thanks to DvS for this). The .itp file for the polarizable water has a [defaults] line that looks like: [ defaults ] LJ Geometric whereas when the OPLS-AA forcefield .itp files