.
You may try dos2unix
On Thu, Feb 24, 2011 at 8:07 PM, Sergio Manzetti
sergio.manze...@vestforsk.no wrote:
No. It contains a charged Gandolinium ion in the middle of a buckyball.
On Fri, Feb 25, 2011 at 2:59 AM, TJ Mustard musta
You have a no charge triplet? Is this a carbene?
TJ Mustard
C -0.677394 -0.928398 -3.166238 C 0.672998 -0.928446 -3.166308
C 1.090287 0.355662 -3.166349
C -0.002252 1.149252 -3.166236
C -1.094761 0.355692 -3.166308
C -2.207300
you will want to use more.
Please email me with questions if you need more.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
PS more below
On February 14, 2011 at 8:54 PM Moeed lecie...@googlemail.com wrote
TJ Mustard
Email: musta...@onid.orst.edu
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is nice.
Please let me know your comments/point of view about the system and setting I am using.
Thanks
Moeed
TJ Mustard
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.
Does anyone have an idea what is happening?
And if you do, can you please give a recommendation?
Thank you,
TJ Mustard
musta...@onid.orst.edu
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On February 12, 2011 at 5:35 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/02/2011 11:49 AM, TJ Mustard wrote:
Hi all,
I have been testing the ability of taking a sphere of a protein around
to the Yahoo! Mail QA for great tips from Yahoo! Answers users.
TJ Mustard
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On February 12, 2011 at 9:31 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/02/2011 3:57 PM, TJ Mustard wrote:
On February 12, 2011 at 5:35 PM Mark Abraham mark.abra
On February 12, 2011 at 10:14 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/02/2011 5:03 PM, TJ Mustard wrote:
On February 12, 2011 at 9:31 PM Mark Abraham mark.abra
of doing this I would be very happy.
Thank you,
TJ Mustard
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Please
by specifying them with the argument r_#_#_#_#_#_#... etc in make_ndx, which can then be used to make a positional restrain file via makerestr. I am just hoping there is a better, more automated way of doing this.
Thank you,
TJ Mustard
On February 11, 2011 at 10:30 AM
Justin,
Ok, if I find a way I will post it back here. And thank you for the recommendations.
Thank you,
TJ Mustard
On February 11, 2011 at 11:05 AM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote
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TJ Mustard
Email: musta...@onid.orst.edu
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Dawei,
I have no problems with proteins in the thousands of atoms. Can you post your command line and mdp files?
Thank you,
TJ Mustard
On February 7, 2011 at 9:31 AM Da-Wei Li lida...@gmail.com wrote:
Well
Da-Wei,
Do you need FEP information on the PR step? Are you going to do a MD(sd) with FEP on after the PR?
And are you doing hydration of a protein?
Thank you,
TJ Mustard
On February 7, 2011 at 10:23 AM Justin A. Lemkul
On Mon, Feb 7, 2011 at 1:31 PM, TJ Mustard musta...@onid.orst.edu wrote:
Da-Wei,
Do you need FEP information on the PR step
and protein, what I wish to know is if this will cause artifacts in my system?
Thank you,
TJ Mustard
musta...@onid.orst.edu
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I can add my .mdps but I do not think they are the problem since I know it works on my personal iMac.
Thank you,
TJ Mustard
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On January 25, 2011 at 2:08 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 26/01/2011 5:50 AM, TJ Mustard wrote:
Hi all,
I am running MD/FEP on a protein-ligand system with gromacs 4.5.3
On January 25, 2011 at 3:24 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
On January 25, 2011 at 2:08 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 26/01/2011 5
On January 25, 2011 at 3:54 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 01/26/11, TJ Mustard musta...@onid.orst.edu wrote
On January 25, 2011 at 3:53 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
snip
1. Do the systems in question crash immediately (i.e., step zero) or
do they run
for some time
On January 18, 2011 at 12:50 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 19/01/2011 7:33 AM, TJ Mustard wrote:
On January 17, 2011 at 3:48 PM Mark Abraham mark.abra
On January 17, 2011 at 3:48 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 18/01/2011 10:27 AM, TJ Mustard wrote:
On January 17, 2011 at 2:47 PM TJ Mustard musta
minimization. This happens on our cluster and on our iMacs.
Any help would be appreciated. Also I can attach my mdp files.
Thank you
TJ Mustard
Email: musta...@onid.orst.edu
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The jobs will continue on and finish but we are worried about the error that could be included with these errors.
Any help would be appreciated. Also I can attach my mdp files.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
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On January 17, 2011 at 1:20 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
Hi all,
I have been running alot of simulations on protein ligand interactions,
and my
No this is a completely different error that occurs when the other (EM) error does not.
Thank you,
TJ Mustard
On January 17, 2011 at 1:51 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote
On January 17, 2011 at 2:15 PM TJ Mustard musta...@onid.orst.edu wrote:
No this is a completely different error that occurs when the other (EM) error does not.
Thank you,
TJ Mustard
On January 17, 2011 at 2:21 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
No this is a completely different error that occurs when the other (EM)
error does not.
So, EM
is minimized.
I have also had this issue in our scripts before and I made sure to fix and check all others at that time.
Thank you though,
TJ Mustard
Email: musta...@onid.orst.edu
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On January 17, 2011 at 2:47 PM TJ Mustard musta...@onid.orst.edu wrote:
On January 17, 2011 at 2:21 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote
go away the 1-4 interaction warning might disappear as well.
TJ Mustard
Email: musta...@onid.orst.edu
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for your reply
Sincerely yours
Mohsen
TJ Mustard
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?
for example I want to have a pdb file which contains my protein and one Na and one Cl ion.
by pymol?How?
by manipulating pdb file?How?
Thanks in advance
TJ Mustard
Email: musta...@onid.orst.edu
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.
Hope this helps,
TJ Mustard
On December 28, 2010 at 8:26 AM nikhil damle pdnik...@yahoo.co.in wrote:
Hi,
I am trying to simulate a dimeric structure and I have already simulated its monomeric
on this answer)
How precise is enough? (standard deviations of less than 2 kJ/mol in BAR?)
Currently we are running long (2.5ns) relaxation MDs with no FEP and then running FEP on them for various times, hoping this will decrease any errors we are seeing.
Thank you,
TJ
Hi,
I am trying to speed up my parallel processor Gromacs jobs and was wondering what were the known settings for PME cut-off and PME grid spacing? As of now I am running with a PME cutoff of 0.8 and a fourierspacing of 0.12.
Thank you,
TJ Mustard
be happy to be a/the guinea pig on this one.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
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jobs to a node without telling gromacs (ie. mdrun) how many cpus to use, all the jobs will use all the cpus simultaneously. This can cause job failure.
All the best,
fancy
TJ
On October 28, 2010 at 4:11 AM TJ Mustard musta...@onid.orst.edu wrote:
On October 28, 2010 at 4:05 AM fancy2012 fancy2...@yeah.net wrote:
Dear GMX users
it to gmx-users-requ...@gromacs.org.
Cant post? Read http://www.gromacs.org/Support/Mailing_Lists
TJ Mustard
Email: musta...@onid.orst.edu
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.
Thank you,
TJ Mustard
You can also find some info on the gmx-users mail log/forum by searching for FEP gromacs on google. It is somewhat hard to find but it can be found.
On October 20, 2010 at 9:22 PM Marcelo Brando brandao.marc...@gmail.com wrote:
Hello
the next guy some heartache and precious time.
Thank you again,
TJ Mustard
Roland
On Tue, Sep 28, 2010 at 12:54 PM, TJ Mustard musta...@onid.orst.edu wrote
Hello all,
Is there a argument that will select SOL as the defualt selection for ion substitution? I read the manual and found nothing.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
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On October 1, 2010 at 7:16 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
Hello all,
Is there a argument that will select SOL as the defualt selection for
ion
.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
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Please don't post
I run them.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
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? Read http://www.gromacs.org/Support/Mailing_Lists
TJ Mustard
Email: musta...@onid.orst.edu
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. The topsort.c file in the source code was missing a line of code and I was getting Improper Dihedral in ip_pert errors. I have run several methane hydration FEPs with very similar results. I am hoping this is a small problem that can be fixed easily.
Thank you for any assistance,
TJ Mustard
Yes -dlb no not on and I will file a bugzilla. Thanks again Berg Hess.
TJ Mustard
On September 20, 2010 at 8:38 PM Berk Hess g...@hotmail.com wrote:
Hi,
Could you file a bugzilla?
And what do
searched for this on google and found nothing. Do I need an Improper Dihedral section in my top/itp file? I have ran this same system with fep off and it runs perfectly.
Any help is much appreciated.
TJ Mustard
Email: musta...@onid.orst.edu
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Thank you both.
I have set up soft core parameters for this test. All I want is an actual test to work at this point.
On September 15, 2010 at 5:31 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote
:
- Original Message -
From: TJ Mustard musta...@onid.orst.edu
Date: Tuesday, September 14, 2010 10:54
Subject: [gmx-users] FEP top file setup...
To: gmx-users@gromacs.org gmx-users@gromacs.org
in advance,
TJ Mustard
Email: musta...@onid.orst.edu
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Please don't post (un
in GROMACS 4.5.
Any help would be much appreciated.
TJ Mustard
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My appologies I have errors all over this.
On September 11, 2010 at 12:44 AM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
Downloaded a pdb from pdb.org (1HNX
.
Thank you in advance,
TJ Mustard Email: musta...@onid.orst.edu
Cell: 509-879-4173
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TJ Mustard
Email: musta...@onid.orst.edu
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On September 9, 2010 at 9:11 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
First
My one thought is that it is to large of a system for GROMACS to run it, yet I have run a small protein in GROMOS96-43a1 and it works but not in any of the AMBER force fields.
On September 9, 2010 at 9:35 PM TJ Mustard musta...@onid.orst.edu wrote
On September 9, 2010 at 10:04 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
snip
*Positional restraint mdp file:*
define = -DPOSRES
constraints
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