[gmx-users] Steepest Descents converged to machine precision in 7559 steps, but did not reach the requested Fmax < 100.

Dear Gromacs experts, I am running gromacs for the first time, and this is my em.mdp file. define = -DFLEXIBLE constraints = none integrator = steep dt = 0.01 ; ps ! nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier

[gmx-users] Bus error (core dumped)

Dear GROMACS experts, I run mdrun with this command: //mdrun -ntomp 8 -ntpi 1 -v -s em.tpr -deffnm em After Step 67, it was terminated with a Bus error (core dumped). Can anyone please explain this? Thanking you in advance. -- View this message in context: http://gromacs.5086.n6.nabble.co

[gmx-users] Output for rmsd and radius of gyration doubts

Hi, Just need some advice regarding the following results I obtained while following the tutorial from this site, using a protein structure that I modelled using Modeller. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ 1. My output plot of RMSD doesn't converge.

[gmx-users] Re: Output for rmsd and radius of gyration doubts

Dear Justin, Oh, no wonder. Thank you so much for your prompt reply! :) Best wishes. -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5005885.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

[gmx-users] mpirun: cannot open .tpr file

Hi, I'm trying to test mpirun, so I tried with the NPT equilibration. From the tutorial of: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html I run this command: mpirun --np 10 --hostfile ~/hostfile mdrun_mpi -npme 3 -deffnm npt and obtained an error

[gmx-users] Re: Output for rmsd and radius of gyration doubts

Hi Justin, I tried running the simulation for 10ns and this time, my RMSD graph shows a stable fluctuation of 0.45nm from 2.5ns to 10ns. The radius of gyration shows stable fluctuation from 4ns to 10ns around 2.46nm. My doubt is, shouldn't the RMSD be fluctuating at 0.1nm? Does it mean that my str

[gmx-users] Re: Output for rmsd and radius of gyration doubts

Hi Justin, Thank you for your prompt reply! As this is my first approach to molecular dynamics, I still have lots of to understand but I'm constantly reading and trying to work things out. I predicted 2 structures, one using Modeller, and another one with I-Tasser. I followed your very informative

[gmx-users] Re: Output for rmsd and radius of gyration doubts

Thank you so much, Justin! Yes, I will do so. :) Take care. Best wishes. -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5006087.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users

[gmx-users] trjconv centre protein

Hi, I know this question has been asked for a few times already but I don't seem to get it. :( I did: 1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron 2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top 3) grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

[gmx-users] Re: trjconv centre protein

HI Justin, Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the protein has to be in the center (inside the box) before the simulation, is it? Thank you. Best regards. -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454

[gmx-users] Re: trjconv centre protein

Crystal clear! Thank you Justin! :) Take care. Regards. -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454p5006459.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] genion

Hi, Just wondering. My system shows this: "System has non-zero total charge: 11.98" and thus, I use the command as below to add 12 Cl to the protein: "genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn 12" However, when I checked the genion.log file, it shows that th

[gmx-users] Re: genion

Hi Justin, Thank you for your prompt reply! My grompp goes like this: "grompp -f minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr" Is it in the topol.top file? The reason I'm asking this is because I obtained this error while running MD: "Fatal error: 2 particles communicated to PME node 2

[gmx-users] Re: genion

Hi Justin, Yup, the grompp works fine. :) Gotta figure out on the Blowing Up now. (>.<) Thank you once again! Take care. -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916p5007924.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

[gmx-users] proceed from output of MD

Hi, I have run a 20ns MD simulation on my protein structure and about to proceed with Autodock. I am wondering if I have missed anything. The output of the file is gro, so I converted it to a pdb file. Then, when I process it with Autodock Tools, all I get is the water molecules surrounding my pro

[gmx-users] Re: proceed from output of MD

Hey, I have figured that out! My bad! :D Thank you. Best regards -- View this message in context: http://gromacs.5086.x6.nabble.com/proceed-from-output-of-MD-tp5008364p5008368.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@g