[gmx-users] problem in running grompp

hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows -

Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5

Hi, For the record there is also the -reprod (reproducibility) that also turns off the dynamic FFTW plan optimization. With these options enabled you will lose a bit of performance, but should get binary identical runs even in parallel (as long as you use the same number of CPUs). Cheer

[gmx-users] how to include Fe-S topology in .rtp file

hi all...   I am simulating a protein with Fe-S cluster. What is the protocol for generating a .rtp file with Fe-S topology...As i am using ffG43a1 forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and dihedral type... but it is not there..what i should do?..   If anyone have the

[gmx-users] about epsion_surface

Dear, I do not know where should I have to use the epsion_surface? The system include a CG membrane, a charged macromolecule above the membrane and some counterions ? It is suitable to using this parameter epsilon_surface = 1? It is appricated if some one tell me something about how to use this

[gmx-users] how to run with mpi?

i have a small cluster of 3 computers, 1 master and 2 slaves, running Rocks 4.2.1 and Gromacs 3.3.1. Are there any good tutorials about how to use openmpi and Gromacs? I'm rather new to this so any help would be amazing. Thank you :)

Re: [gmx-users] Scaled 1-5 interactions

On Sun, Jun 07, 2009 at 05:35:14PM +0200, Florian Dommert wrote: > Glad to hear the my help works. Setting the LJ parameters zero for the > should avoid a further contribution of the LJ part from the defined 1-5 > IA, since they are already present in the nonbonded part of the > interaction types.

Re: [gmx-users] Scaled 1-5 interactions

* Borys Szefczyk [2009-06-07 14:12:14 +0200]: On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote: * David van der Spoel [2009-06-06 08:06:26 +0200]: The VDW may work, but not differently scaled 1-4 and 1-5 coulomb interactions. Where is the matter if I have a [ pairs ] direct

Re: [gmx-users] reg aCTIVE SITE

Quoting vidhya sankar : > Dear gromacs users, >   Is there is any tools available in > gromacs to predict active site of protein molecule ?   othewise how could we > predict active site of a protein molecule  > please let me know .   i am  waitingfor your positive r

[gmx-users] reg aCTIVE SITE

Dear gromacs users,   Is there is any tools available in gromacs to predict active site of protein molecule ?   othewise how could we predict active site of a protein molecule  please let me know .   i am  waitingfor your positive reply Bollywood news, movi

Re: [gmx-users] Scaled 1-5 interactions

On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote: > * David van der Spoel [2009-06-06 08:06:26 +0200]: >> The VDW may work, but not differently scaled 1-4 and 1-5 coulomb >> interactions. > > Where is the matter if I have a [ pairs ] directive in the itp file like > this : > > >

Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5

Jim Kress wrote: I've been doing multiple runs using gromacs v 4.0.5 mdrun and a constant topol.tpr input file. Unfortunately, the results that I get in my md.log differ from run to run. This is due to dynamic load balancing. Due to fluctuations in the CPU usage (e.g. due to operating system)