[gmx-users] recalculating .trr from .xtc

Dear GROMACS users, Does anyone know how significant is the difference between the "original" .trr file from a simulation and a "recalculated" .trr from a whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)? I mean... do you know how big would be the error induced by this "recalculatio

[gmx-users] Accounting for the solvent with -rerun?

tory decompositions and energy recalculations. Thank you in advance, Leandro Bortot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don&#x

[gmx-users] g_energy units

eatly appreciated. Thank you in advance, Leandro Bortot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe request

[gmx-users] gmx 4.6 does not detect GPUs, but 4.5 does

Dear all, I have just updated the GROMACS installation at a local cluster which have 2 GPUs. I installed CUDA 5 with no problems and it was detected by cmake. No problems during installation. With GROMACS 4.5 I was able to use the GPUs of this same cluster, but now GROMACS 4.6 says that

[gmx-users] Coupling only a variable solvent subgroup to the thermostat

so much in 5ps. Maybe I can make a new index file each, say, 20ps. Any suggestions and/or comments about how to do this and my proposed script would be very helpful. Thank you in advance, Leandro Bortot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

Re: [gmx-users] RMSD

you can make a simple script which calculates all the pairwise RMSD values with g_rms. By doing this you can make a "RMSD matrix". The usefulness of this depends on what you are trying to see, which wasn't clearly stated to us. I did it once because I wanted to know how similar the 20 co

Re: [gmx-users] hybrid solvent model

I'm also interested in doing this with GROMACS but couldn't find a way yet. In my case I'm interested in applying it to REMD simulations in which large conformational changes occur, which makes the implementation more difficult because the shape of the water layer would be irregular and change

Re: [gmx-users] how to indicate solvent flexibility?

My first thought was to compare the diffusion of the bulk and internal waters with g_msd. You said that in some case the internal waters forms hydrogen bonds with the protein. I think that in this case a plot showing this would be nice too. 2013/1/8 Justin Lemkul > > > On 1/8/13 11:4

Re: [gmx-users] Re: Simulation of 2D lattice model

Hi Starlight, I had an idea right now... Maybe if you freeze every atom of your system only in one dimension you will get a good approximation of a 2D system. Of course you would need to make the coordinates accordingly, e.g. placing the system in the x-y plane and freezing the z dimension. I

Re: [gmx-users] conformational change

s are related to the helix destabilization. I used VMD to get the residue numbers of the waters from the .gro file of the whole system (there were some issues with pymol), then I removed such residues from the .gro file of the box and adjusted the topology accordingly. I hope it helps, Leandro Bo

Re: [gmx-users] Re: Pulling ion - US

I have made SMD simulations in order to separate a Ca2+ ion from its complexation site in the protein, which had charge of about -6 e. Without position constraints in the protein alpha carbons it unfolded in every pull simulation. 2012/12/11 Thomas Schlesier > wont happen, since the prob

Re: [gmx-users] GBSA with ligands

for you ligand. > > Which Acpype does is to create/convert Amber/GAFF parameters to usual MD in > Gromacs. > > Alan > > On 12 October 2012 11:34, Leandro Bortot wrote: > > > Dear users, > > > > After parametrizing a ligand with antechamber and converting

Re: [gmx-users] genion problem with divalent ions

Hi there, In addition to setting -pq to 2 as Justin said, you can set -conc to a very low value such as 0.1 for neutralizing the system. One more thing... genion apparently uses the box volume when determining how many ions are necessary for getting a given ionic strength. However,

Re: [gmx-users] Glycoproteion MD

Hi Guang, You can use the GLYCAM force field, which has parameters for carbohydrates and glycoproteins compatible with AMBER99. You can get the AMBER topology and structure files directly from their web interface, the "Online Glycoprotein Builder" ( http://glycam.ccrc.uga.edu/ccrc/gp/

[gmx-users] System neutralization in Thermodynamic Integration

tem charge increases until it is +1 when lambda=1. I am using 1 nm cutoff for the non-bonded interactions and PME. Should I make something to account for this total system charge? Won't it induce artifacts in my calculation? thanks in advance, Leandro Bortot -- gmx-users mailing li

[gmx-users] Replica Exchange with GPUs

plica Exchange Molecular Dynamics (REMD) with the GPUs. I suppose each GPU can be used to run a replica, is this possible? thanks in advance, Leandro Bortot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are al