[gmx-users] [solved] Problem compiling Gromacs 4.6 on BlueGene/Q

>> >> 1. Compile FFTW-3.3.2: >> ./configure --prefix=/scratch/home/user/fftw-3.3.2 >> make && make install >> > > This does not compile a single-precision FFTW (per generic GROMACS > installation instructions). Hi Mark, Thanks for pointing it out. I recompiled FFTW like so: ./configure --prefix=

[gmx-users] RE: About the binary identical results by restarting from the checkpoint file

Hi GROMACS Users, I am sorry if you are bothered by my second post about this topic. But the fact is that I tested restarting simulations with .cpt files by GROMACS 4.6.1. and I still cannot get binary identical results from restarted simulations with those from continuous simulations. The co

[gmx-users] System equilibrium problems

Hi everyone, I recently tried to perform an 25 ns simulation on 12 nodes and was greeted with this error around 3.2 ns into the run. '3 particles communicated to PME node 9 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.' To my knowl

[gmx-users] Tabulated Potentials

Hello Users, Recently I have been trying to implement the use of tabulated potentials in GROMACS to an system of argon atoms. I run a NVE simulation of 1000 argon atoms and then plot the potential energy from the output. ar.itp : [ defaults ] ; nbfunccomb-rule gen-pairs fu

Re: [gmx-users] Problem in RMSD plot

On 6/13/13 10:47 AM, Sainitin Donakonda wrote: Hi, Recently i ran 20ns protein ligand simulation ..in cluster ..I ran it in 2 parts first i ran 10ns and extended to another 10ns.. Then I got 2 .xtc files...i combined both these trajectories using following command trjcat -f 1.xtc 2.xtc -o co

Re: [gmx-users] Fw: charmm27 in gromacs- grompp error

On 6/13/13 12:37 AM, Revthi Sanker wrote: Dear all, I am using charmm27 forcefield in gromacs for performing all atom simulations (system comprising of DOPC, cholesteryl ester and protein) .I got the itp file for dopc from the lipid book in which they have mentioned #include "charmm27.ff/f

[gmx-users] Problem in RMSD plot

Hi, Recently i ran 20ns protein ligand simulation ..in cluster ..I ran it in 2 parts first i ran 10ns and extended to another 10ns.. Then I got 2 .xtc files...i combined both these trajectories using following command trjcat -f 1.xtc 2.xtc -o combine.xtc -cat Then using combine.xtc i plotted RM

[gmx-users] Re: distance_restraints

Hi, Tsjerk I want equlibration enough time, so set NVT time 10ns , but simulation collapse at 7ns, protein have 7 fragments. Before NVT, I just do one time of steep energy minimization. So, I want first use constraint do steep, cg in vacuum, then add water, do steep, cg with constraint, then

Re: [gmx-users] Re: distance_restraints

Hi Maggin, Why do you run EM with constraints? Cheers, Tsjerk On Thu, Jun 13, 2013 at 10:53 AM, maggin wrote: > Hi, Justin, > > It's seems no problem at steep energy minimization, except lose H atoms > connect with C, the superposition are very well. > > When I use Pymol to align the NMR st

Re: [gmx-users] Problem compiling Gromacs 4.6 on BlueGene/Q

On Thu, Jun 13, 2013 at 10:13 AM, Jernej Zidar wrote: > Hi, > I'm trying to compile Gromacs 4.6 on a BlueGene cluster but I've > stumbled upon something that looks like a bug. > > Here's how I'm trying: > > 1. Compile FFTW-3.3.2: > ./configure --prefix=/scratch/home/user/fftw-3.3.2 > make && m

[gmx-users] Re: distance_restraints

Hi, Justin, It's seems no problem at steep energy minimization, except lose H atoms connect with C, the superposition are very well. When I use Pymol to align the NMR structure and the structure after cg minimization, because cg is after steep, so same as steep, they lose H atoms that connect wi

[gmx-users] Problem compiling Gromacs 4.6 on BlueGene/Q

Hi, I'm trying to compile Gromacs 4.6 on a BlueGene cluster but I've stumbled upon something that looks like a bug. Here's how I'm trying: 1. Compile FFTW-3.3.2: ./configure --prefix=/scratch/home/user/fftw-3.3.2 make && make install 2. Compile Gromacs 4.6 using instructions from Gromacs' pag

[gmx-users] Re: distance_restraints

Hi, Justin, I use Pymol to align the NMR structure and the structure after steep minimization, find problematic areas are superposition very well, while all the problematic areas have same character, that after steep minimization, Amino acid will lose some H atoms connect with C