Quoting David Mobley <[EMAIL PROTECTED]>:
> Which gromacs version are you using?
Version 3.3.1 (forgot to mention that before, sorry!)
>
> I vaguely remember, that at one point I may have found a bug relating
> to atoms that initially started out with no charges and then had
> charges that were
Hi all,
I am trying to understand what type of distance can be used with g_cluster?
In the manual, it is written that RMS deviation after fitting or RMS deviation
of atom-pair distances can be used to define the distance between structures in
the first paragraph.
However, in the "other options
Justin,
Following up on this, I looked back through my old e-mails and found
that, indeed, you do appear to be running into a known bug. It's one I
helped a guy named Bharat find, so the relevant bugzilla is from him
rather than from me: http://bugzilla.gromacs.org/show_bug.cgi?id=175.
It appears
Dear Justin,
> I'll preface this message by saying that this is my first foray into free
> energy
> calculations, and I am hoping that someone more well-versed in the matter may
> be
> able to help me sort out some strange results. I have done a good bit of
> reading in terms of tutorials and i
Hello all,
I'll preface this message by saying that this is my first foray into free energy
calculations, and I am hoping that someone more well-versed in the matter may be
able to help me sort out some strange results. I have done a good bit of
reading in terms of tutorials and in the archives,
Thanks a lot, you guys :-)
Hui
> Message: 2
> Date: Sat, 16 Feb 2008 07:30:03 +0100
> From: "Tsjerk Wassenaar"
> Subject: Re: [gmx-users] How to ask pdb2gmx to print all parameters in
> the itp file
> To: "Discussion list for GROMACS users"
> Message-ID:
>
> Content-Type: text
The reason I commented about the use of your .tpr file is that, from your
message, it seemed that you did not understand exactly how to use trjconv, and
were perhaps using a different .tpr file (named topol.tpr) to simply satisfy
trjconv. Your previous message said your grompp output produced a m
Justin I already tried this
I tried this command--->
trjconv -f myprotein.trr -o trajout_whole.trr -pbc whole
this was showing this error
"can not open file
topol.tpr"
then
I repeated the same command with "-s topol.tpr"
then
trjconv -f trajout_whole.trr -o trajout_nojump.
xi zhao wrote:
> Dear sir :
> Can you tell me a detail of procedure, I have only chromophore molecular
> top,but I need entire top and gro for pdb + chromophore!
Your use of terminology is unclear - and you can't afford this sort of
lack of clarity in science. pdb, gro and top are all generic fi
Quoting xi zhao <[EMAIL PROTECTED]>:
> Dear sir :
> Can you tell me a detail of procedure, I have only chromophore molecular
> top,but I need entire top and gro for pdb + chromophore!
I would invest some serious time in background reading on conducting MD,
especially with Gromacs, as there are
Dear sir :
Can you tell me a detail of procedure, I have only chromophore molecular
top,but I need entire top and gro for pdb + chromophore!
Mark Abraham <[EMAIL PROTECTED]> 写道：
xi zhao wrote:
> Dear all users:
> I want to simulate a system ( protein + chromophore). I
> have had chromophore
xi zhao wrote:
> Dear all users:
> I want to simulate a system ( protein + chromophore). I
> have had chromophore.gro and its top file using amb2gmx.pl,but I find I
> can not use them to translate PDB( protein + chromophore) file into gro
> and top files properly. So I need your advice about fu
Dear all users:
I want to simulate a system ( protein + chromophore). I have had
chromophore.gro and its top file using amb2gmx.pl,but I find I can not use them
to translate PDB( protein + chromophore) file into gro and top files properly.
So I need your advice about further procedure!
Than
Hi Erik,
Did you put up a registration page for the workshop?
Could you give information, if there is any, about the workshop that will be
held in Göttingen? I am outside of the countries you mentioned :)
-Original Message-
From: Erik Lindahl <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
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