Dear Dwey,
Please direct questions like this to the gromacs user list, after asserting
that the answer has not already been given. In addition, please read
http://md.chem.rug.nl/~mdcourse/molmod2012/md.html
Regards,
Tsjerk
On Tue, Oct 8, 2013 at 5:35 PM, Dwey wrote:
> Dear Tsjerk,
>
>I s
Original-Nachricht
> Datum: Wed, 18 Apr 2012 08:18:27 -0400
> Von: "Justin A. Lemkul"
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] Re: Questions WHAM
>
>
> lloyd riggs wrote:
> > Original-Nachricht --
lloyd riggs wrote:
Original-Nachricht
Datum: Wed, 18 Apr 2012 03:13:09 +1000 Von: Mark Abraham
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Re: Questions
On 18/04/2012 12:10 AM, lloyd riggs wrote:
Included below (although Im terrified youll invalidate
Original-Nachricht
> Datum: Wed, 18 Apr 2012 03:13:09 +1000
> Von: Mark Abraham
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] Re: Questions
> On 18/04/2012 12:10 AM, lloyd riggs wrote:
> > Included below (although Im terrified you
On 18/04/2012 12:10 AM, lloyd riggs wrote:
Included below (although Im terrified youll invalidate massive parallel work
with a single comment) is the .mdp file I used for 10 of the runs, basically it
was the only way I could get it to run. The time step is small because of the
small molecule i
I solved the problem on a Linux machine, with about all the text editors, I was
stuck for days on a PC, which even the script editors couldn't spot a
difference in files. all i used was ms txteditor to cut and paste.
> I dont know. All I know is if I have it print one of the other deminsions,
> I dont know. All I know is if I have it print one of the other deminsions, I
> get the other curves mentioned.
>
"When accusing the code of doing something wrong, "I don't know" isn't a very
good justification ;) The contents of pullx.xvg are the COM coordinates of the
reference group on t
lloyd riggs wrote:
Original-Nachricht
Datum: Tue, 17 Apr 2012 07:49:06 -0400
Von: "Justin A. Lemkul"
An: lloyd riggs , Discussion list for GROMACS users
Betreff: Re: Questions
lloyd riggs wrote:
Dear Justin,
So I get no answere on the mail list so decided to ask you
Original-Nachricht
> Datum: Tue, 17 Apr 2012 07:49:06 -0400
> Von: "Justin A. Lemkul"
> An: lloyd riggs , Discussion list for GROMACS users
>
> Betreff: Re: Questions
>
>
> lloyd riggs wrote:
> > Dear Justin,
> >
> > So I get no answere on the mail list so decided to ask y
lloyd riggs wrote:
Dear Justin,
So I get no answere on the mail list so decided to ask you (and most likely
Dr. Abrahams if you dont answere) some questions as follows.
Please keep all discussion on the mailing list.
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
Your
Hi Tsjerk,
Thank you for all the clarifications. Just one more thing, I excluded the
loop residues with RMSF>4 A. (because their movement is dominated by random
diffusion), did PCA on the rest of the protein, and the cosine content
improved significantly. Is this procedure acceptable?
Thanks in a
Hi Thomas,
First of all, proteins in solution don't suddenly stop with Brownian
motion at some point. It's just the way things move at the microscopic
level. Second, the cosine content has nothing to do with randomness.
Really. Nothing. On the contrary. The cosine content indicates
unidirectional
Dear Tserk and the rest of GROMACS users,
Last time I measured the cosine content of different time intervals from
the PCs of the whole trajectory. This time I did PCA for each time interval
and measured the cc which is the right way I suppose. Maisuradze et al.,
2009 claim that a CC value below 0
Hi Thomas,
Whether or not it makes sense to do PCA on the domain only depends on
the question you ask. It may well make sense if you aim at
characterizing the intra-domain motions. But be aware that you will
view those motions within the context of the rest of the protein. It
is quite likely that
Regarding my second question, I have been experimenting with the cosine
content using different portions of the trajectory and these are the
results I got for the first principal component:
proj-ev1_coscont_0-5ns.xvg 0.0174761
proj-ev1_coscont_0-10ns.xvg 0.0283423
proj-ev1_coscont_0-15ns.xvg 4.169
Dear all,
Thank you very much Chris, Xavier and ms (;) for your comments and I will take
into account your suggestions in my proposal (for GENCI, Chris ;)) .
A bientot
Stefane
--
Message: 1
Date: Thu, 14 Oct 2010 17:22:
Hi Lin,
> 1. Although you have explained the differece between HOH, AHOH and
> BHOH, I do not fully understand. => Can I delete all of atoms,
> HOH, AHOH and BHOH ?
You can delete one of them, either A or B, if you want to include the
water in your model. It may be that pdb2gmx discards the B
Chih-Ying Lin wrote:
Hi Tsjerk:
I still have questions here.
1. Although you have explained the differece between HOH, AHOH and
BHOH, I do not fully understand. => Can I delete all of atoms,
HOH, AHOH and BHOH ?
2. So, in your tutorial, you use "united atom" algorithm, right?
and, "pdb2gmx"
Hi Tsjerk:
I still have questions here.
1. Although you have explained the differece between HOH, AHOH and
BHOH, I do not fully understand. => Can I delete all of atoms,
HOH, AHOH and BHOH ?
2. So, in your tutorial, you use "united atom" algorithm, right?
and, "pdb2gmx" can recognize the "uni
Hi Lin,
I bounce this mail to the gromacs user list as the issues are well off
to be archived.
> I have two stupid questions here.
Well, that's up to us to decide ;)
> 1. I want to get the proper structure of lysozyme.
>
> From your tutorials, 1LW9.pdb file is used. Potassium (K), chloride (CL)
Hi Periole, May be this website is useful for implicit solvent calculations.http://apbs.sourceforge.net/mohanOn 17/04/06,
[EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
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