[gmx-users] removal of the initial periodicity by editconf

Dear Justin I study your tutorial ( KALP15 in DPPC). You had said Convert the dppc128.pdb to .gro format with editconf and remove the initial periodicity. Which of following lines shows removal of the initial periodicity: 1) editconf -f dppc128.pdb -o dppc128.gro 2) editconf -f dppc128.pdb -o

[gmx-users] removal of the initial periodicity by editconf

Dear Justin Excuse me for my previous question. I should use trjconv to remove initial periodicity. But I have another problem: when I use editconf -f dppc128.pdb -o dppc128.gro I encounter with Fatal error: Unknown atomtype OW I did all steps based on tutorial. What is the problem? Best

[gmx-users] removal of the initial periodicity by editconf

Excuse me. when I use grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I encounter with Fatal error: Unknown atomtype OW -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] removal of the initial periodicity by editconf

On 6/22/13 8:59 AM, Andrew Bostick wrote: Excuse me. when I use grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I encounter with Fatal error: Unknown atomtype OW Apparently something has gone wrong when editing the force field files. I don't know what would have led you

[gmx-users] Gromacs GPU system question

Hello, I am assembling a GPU workstation to run MD simulations, and I was wondering if anyone has any recommendation regarding the GPU/CPU combination. From what I can see, the GTX690 could be the best bang for my buck in terms of number of cores, memory, clock rate. But being a dual GPU card,

Re: [gmx-users] Gromacs GPU system question

On 22.06.2013 17:31, Mare Libero wrote: I am assembling a GPU workstation to run MD simulations, and I was wondering if anyone has any recommendation regarding the GPU/CPU combination. From what I can see, the GTX690 could be the best bang for my buck in terms of number of cores, memory,

Re: [gmx-users] Gromacs GPU system question

On 22.06.2013 22:18, Mare Libero wrote: The vendor I contacted was pushing for one of the high end i7 processors with hyper-threading. But from what I can read, most of the MD software don't make any use of it. So, using a the multi-cores AMD (like your FX-8350) can be a cheaper and more

[gmx-users] Re: free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2

Hi Justin, Thank you for sharing your experience with me. As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box and I am able to reproduce a similar result ( DG= -9.30 kJmol-1). Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while Gromacs ver 4.5.7 as