Date: Wed, 11 Jul 2012 10:32:35 +0200
From: Tsjerk Wassenaar
Subject: Re: [gmx-users] Re: Water molecules cannot be settled, why?
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset=UTF-8
> Hi John, Check where the unsettling water molecule is placed.
> If it'
Hello, everyone,
I am reviving a discussion I started about a month back.
http://gromacs.5086.n6.nabble.com/Water-molecules-cannot-be-settled-why-tt4998059.html
I thought that I would try to work around the problem by only proceeding
with those simulations that didn't crash, but I've reached
Recently I have started to get crash messages in my molecular dynamics
runs which look like this:
Reading file exp37b-prep.tpr, VERSION 4.5.4 (single precision)
Making 1D domain decomposition 5 x 1 x 1
starting mdrun 'Protein in water'
50 steps, 1000.0 ps.
step 81240: Water molecule start
I am starting to write my own turnkey scripts to automate GROMACS (v
4.5.4) work flow. Many of the GROMACS commands, such as pdb2gmx and
genion, have interactive options by default, meaning that you manually
enter information when the program runs.
In the tutorials, we are taught to invoke pd
Following up to myself:
Looking back through the archives, I have learned that the issue of
solvent atoms being exported from trjconv into PDB files as "ATOM"
rather than as "HETATM" is an issue that was raised fully six years ago.
http://www.mail-archive.com/gmx-users@gromacs.org/msg00405.ht
I am trying to import PDB file snapshots from a GROMACS 4.5.4-generated
trajectory into other software tools -- specifically, Biopython. I
generate the snapshots using trjconv in GROMACS.
I am interested in the water molecules from my solvent box, so I do not
discard them. When trjconv promp
Hello everyone,
I've used the rot+trans option in GROMACS trjconv to superimpose groups of
atoms within a single molecular dynamics simulation. I am now interested in
modeling a protein, and a rather thoroughly scrambled circular permutation of
that same protein. I want to construct a superim
Thanks for your advice!
John Ladasky
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
w
8 matches
Mail list logo
