Re: [gmx-users] Finding centroid for a bunch of residues

Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while trying to restrict my MDRUN for a particular site of the protein molecule I want to visualize the site and find out the centroid for t

[gmx-users] Checkpointing GROMACS jobs

Hello, I have been using GROMACS for some very long (in wall clock terms) simulations, and am curious as to how other users on this list solve the problem of checkpointing long MD runs. It's a problem because of the tendency of computational nodes in large HPC facilities (the more processors,

Re: [gmx-users] Re: Targeted MD

Mark Abraham <[EMAIL PROTECTED]> wrote Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed wei-xin xu wrote: > Some hints on practices that generally *not a good idea* to us

[gmx-users] Re: Diagnosing an explosion

Apologies for replying to myself - maybe I can sharpen up some of my original questions below: Reply below > >> I am having a problem with my BD simulation either crashing with a Range >> error or locking up the mdrun process completely. >> >> I am running Gromacs 3.3.1 (must use this versi

[gmx-users] Re: diagnosing an explosion

Reply below I am having a problem with my BD simulation either crashing with a Range error or locking up the mdrun process completely. I am running Gromacs 3.3.1 (must use this version ATM because HPC provider has not upgraded yet) on a quad core Intel machine, w/ Fedora Core 7. I have 1

[gmx-users] Diagnosing an explosion

Hello, I am having a problem with my BD simulation either crashing with a Range error or locking up the mdrun process completely. I am running Gromacs 3.3.1 (must use this version ATM because HPC provider has not upgraded yet) on a quad core Intel machine, w/ Fedora Core 7. I have 1000 'pa

RE: [gmx-users] Coarse-graining and tabulated non-bonded potentials - will write

bject: RE: [gmx-users] Coarse-graining and tabulated non-bonded potentials -will write To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; format=flowed From: Steven Kirk <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gm

[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write up on the wiki

Hello all, Firstly, many thanks to everyone who has contributed useful advice to me over a number of years using GROMACS. I have performed a large number of potential of mean force calculations for the forces acting between two approximately spherical amorphous silica particles (various size

[gmx-users] Energy minimization problem with macromolecule and polarizable water model

Hello, I recently obtained (from DvS) the .itp file for the SSWM4-DP polarizable water molecule, and a corresponding set of water box coordinates. I use double precision executables in all of the calculations mentioned below. I ran an energy minimization on this box of water, then a 500ps

[gmx-users] Making two defaults sections compatible

Hello, I'm using a macromolecule with the OPLS-AA force field, solvated with SSWM4-DP polarizable water (many thanks to DvS for this). The .itp file for the polarizable water has a [defaults] line that looks like: [ defaults ] LJ Geometric whereas when the OPLS-AA forcefield .itp files

[gmx-users] SWM4-DP (Roux group polarizable water model) .itp file needed

Hello, Does anyone on the list have a .itp file for the recent Roux group SWM4-DP polarizable water molecule model? DvS mentioned a couple of months back that recent polarizable water molecule models from this group, and also models from the van Gunsteren group [presumably COS(G?)] work in GR

[gmx-users] Advice needed on choosing a VdW cutoff

Hello, I would be very grateful for advice on the following system: Consider a pair of spherical macromolecules of diameter ~2.5 nm, arranged along an x-axis so that their centres of mass are 4nm apart, then centered in a 14 x 10 x 10 nm periodic box, so that the minimum distance between eith

[gmx-users] Droplet vs. vesicle vs. big periodic box vs. implicit solvent

Hello, I would be grateful if anyone on the list could give me the benefit of their expertise on the following proposed simulation: System: 2 amorphous approximately spherical silica particles of diameter 2.5 nm, each with a net charge of -9e, with about 5 nm spacing between their centers of

[gmx-users] more x2top troubles

Hello, First, let me thank all those who have contributed helpful suggestions here in the past, especially DvS. I am having major problems generating a topology using x2top that contains valid data in the [bonds], [angles] and [dihedrals] sections. The files I use can be downloaded here: h

[gmx-users] Re: problems with x2top

From: David van der Spoel <[EMAIL PROTECTED]> Subject: [gmx-users] Re: Problems with x2top To: Steven Kirk <[EMAIL PROTECTED]>, Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Kirk wrote:

[gmx-users] Handling of charge and mass fields in topology file produced by x2top

Hello, I am using x2top to produce a topology file for a system involving silica in water, and using the OPLS-AA force field, using the v.3.3-1 CentOS x86_64 RPMS provided on the website (do these contain all the latest fixes?). My topology files (suitably edited for brevity, and to insert the a