Re: [gmx-users] error in parallel mdrun

hazizian wrote: hi I want to use mdrun, when i use It as one job it goes on. but when i use as parallel job grompp -np 4 -f md300.mdp -c pr.pdb -p topol.top -o md300.tpr then mpirun -np 4 mdrungromacs_mpi -nice 0 -v -s md300.tpr -o md300.trr -c md300.pdb -e

[gmx-users] Wrong manual on web page

Hi, the manual at ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf gives out the manual version 3.3, could somebody fix this? :) -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632

RE: [gmx-users] distance restraints and domain decomposition

Hi, Is this the only output you got? There is no error message at all? If there was no error message and you get the error quickly (i.e. not after hours of simulations), please file a bugzilla entry, give the exact command line of mpirun and mdrun and attach your tpr file. Berk Date: Fri, 5

[gmx-users] Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

Dear GMX users: I'm facing problems installing Gromacs 4.0.2 with mopac7 QM/MM. I have downloaded MOPAC7 for SourceForge, as linked in previous mails, and installed it. After, MPICH and fftw 3.0.1. So: ./configure --enable-mpi --with-qmmm-mopac runs O.K., but, during make: (some shell

[gmx-users] Re: Accuracy of simulations

najwa drici wrote: I made a MD simulation of solvated protein and i have the out put file md.log , I took the part of R M S - F L U C T U A T I O N S in order to calculating the ratio R = Δ E_tot /Δ E_kin who should be less than 0.05 R = Δ E_tot /Δ E_kin =

[gmx-users] structure factor

Hi, I have problem with calculation structure facor in coarse-grained system using g_rdf -sq, when I use g_rdf I get error message Fatal error: Error: atom (B1) not in list (5 types checked)!. Please help. Thanks in advance. ___ gmx-users mailing list

Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

Laercio Pol Fachin wrote: Dear GMX users: I'm facing problems installing Gromacs 4.0.2 with mopac7 QM/MM. I have downloaded MOPAC7 for SourceForge, as linked in previous mails, and installed it. After, MPICH and fftw 3.0.1. So: ./configure --enable-mpi --with-qmmm-mopac runs O.K., but,

[gmx-users] Is there a way to add protons to all the residues in a given system?

Hi, all, This is probably an obvious question. I did a simulation with an ff53a6 force field, which lacks protons on aliphatic side chains. I have pdb coordinates for each time. Is there a way to add protons to the aliphatic side chains. Your input is appreciated. Sincerely, Art

[gmx-users] Modeling a nickel binding site

Dear All: Could anyone give me an example how to introduce a nickel ion into a protein simulation. I have got a apo-form protein structure and know the approximate coordination for the nickel ion. What I want to do is to run a energy minimization to make the nickel ion in place. However, in

Re: [gmx-users] Modeling a nickel binding site

Xia,Wei wrote: Dear All: Could anyone give me an example how to introduce a nickel ion into a protein simulation. I have got a apo-form protein structure and know the approximate coordination for the nickel ion. What I want to do is to run a energy minimization to make the nickel ion in