[gmx-users] Force field for ions

Dear all: Does anyone know the optimal force field in GROMACS for treating divalent ions in explicit solvent? Would appreciate any recommendations. Thanks, Lili -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Question regarding g_rdf

Hello, I am fairly new to using Gromacs and am writing to seek clarification on the g_rdf module. In the manual, it states that g_rdf calculates radial distribution functions in different ways. The normal method is around a (set of) particle(s), the other method is around the center of mass of a

[gmx-users] question about periodic boundary conditions

Hi, Is there a way to quantitatively determine, from a trajectory file, whether a molecule is interacting with a copy of itself in the adjacent box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure file and viewed the periodic images

Re: [gmx-users] question about periodic boundary conditions

again, Lili On 20 October 2010 13:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy...@yahoo.com wrote: Hi Justin, Thanks for getting back to me. I executed the following command using g_mindist: $gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n index.ndx -od mindist.xvg

[gmx-users] Fatal error: Atomtype Qd not found

Dear GMX users, I have a quick question regarding which Gromacs force field in pdb2gmx is best suited for creating a topology (itp) file for the enzyme, lactate oxidase. So far the force fields in Gromacs 4.0.4 are: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane

Re: [gmx-users] Fatal error: Atomtype Qd not found

/msg14945.html -Lili On 25 March 2010 18:13, Justin A. Lemkul jalem...@vt.edu wrote: rainy...@yahoo.com wrote: Dear GMX users, I have a quick question regarding which Gromacs force field in pdb2gmx is best suited for creating a topology (itp) file for the enzyme, lactate oxidase. So far

Re: [gmx-users] Fatal error: Atomtype Qd not found

it figured out :). Thanks for your concern though. On 25 March 2010 19:22, Justin A. Lemkul jalem...@vt.edu wrote: rainy...@yahoo.com wrote: Hi Justin, I did not mention that I am indeed trying run Gromacs implementing the MARTINI force field. I realize this is not as automatic as selecting

Re: [gmx-users] Segmentation fault while running MD simulation

~ 2009/11/13 Justin A. Lemkul jalem...@vt.edu rainy...@yahoo.com wrote: Hi all, I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy

Re: [gmx-users] Segmentation fault while running MD simulation

...@anu.edu.au rainy...@yahoo.com wrote: Hi all, I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy minimization. I tried to run the inital MD simulation, but the job was cut short due to a segmentation fault, as mentioned

Re: [gmx-users] Segmentation fault while running MD simulation

? Try to find if everything went ok until the segmentation fault by saving log and trajectories. amit On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: rainy...@yahoo.com wrote: Hi, The relevant lines of my script are the following: line 27: # Run MD and write

[gmx-users] Segmentation fault while running MD simulation

Hi all, I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy minimization. I tried to run the inital MD simulation, but the job was cut short due to a segmentation fault, as mentioned in the output file: ^Mstep 0^Mstep