You don't do it the right way. You must start the analysis from the
beginning not from the end of your trajectory. I.e.
0-20ns
0-30ns
0-40ns
...
0-100ns
Until the cosine content of the first 3 principal components that account
for most of the variance in the atomic fluctuation have been dropped a
Hi Thomas,
As I've explained previously, the cosine content does not allow such
inferences. Besides, taking the relaxation from the start into account
in PCA is pretty nonsensical, unless you aim to characterize that
relaxation in the first place. Looking at the cosine content to infer
equilibrati
Hi,
Which version of gromacs are you using. I am applying this tool also to ILs
and it works fine for me in the release-4-5 branch. It is especially strange
that you have a rotational dipole moment of zero. However, currently I have
no idea where the segfault arises. Especially because you get an
Dear Gromacs Users.
I apologize for asking a question that has come up several times by numerous
users in the previous e-mails, but I have read the answers and suggestions to
those posts and I am not still able to solve the problem based on them. It is
completely possible that I am just not
On 25 February 2013 12:14, Tsjerk Wassenaar wrote:
> Hi Thomas,
>
> As I've explained previously, the cosine content does not allow such
> inferences. Besides, taking the relaxation from the start into account
> in PCA is pretty nonsensical, unless you aim to characterize that
> relaxation in the
Hi,
I think my question was misunderstood.
My question is:
Why is second cosine content greater than the other values?
Regards
2013/2/25 Thomas Evangelidis
> On 25 February 2013 12:14, Tsjerk Wassenaar wrote:
>
> > Hi Thomas,
> >
> > As I've explained previously, the cosine content does not a
Hi Thomas,
Okay :) First of all, do be careful that the first stage of
relaxation, giving that nice principal component profile, is not
exclusive. If you take it off, by leaving out the first part of the
trajectory, you may well find that there is another component which is
still relaxing, which m
Because it fits a little bit better to a cosine with full period than
the first one fits a cosine with half period and the third one fits a
cosine with 1.5 period.
Tsjerk
On Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım wrote:
> Hi,
>
> I think my question was misunderstood.
> My question is:
> W
Hello All,
It is a newbie question here, but I can not find a clear response. I would like
to create a simple box of pure DECANE for MD with the Martini force field. I
have tried do that with genbox (as for AA force field)
genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro
Hi Stephane,
martinize.py was written to convert proteins. But you can just take
C2+C5+C8 from atomistic decane and energy minimize against the martini
topology and you'll be fine.
Cheers,
Tsjerk
On Mon, Feb 25, 2013 at 1:39 PM, ABEL Stephane 175950
wrote:
> Hello All,
>
> It is a newbie quest
Hello,
I am using Gromacs VERSION 4.0.7.
Nilesh
> Hi,
>
> Which version of gromacs are you using. I am applying this tool also to
> ILs
> and it works fine for me in the release-4-5 branch. It is especially
> strange
> that you have a rotational dipole moment of zero. However, currently I
> h
On 2/25/13 12:16 AM, Anu Chandran wrote:
Dear users,
I am trying to do a coarse grained simulation of an octamer of a 350
residue protein in water using gromacs-4.5.3 using martini force field. I
got the following error when i started running NPT equilibration
"Step 32, time 0.64 (ps) LINCS W
On 2/25/13 1:01 AM, Jernej Zidar wrote:
Hi.
I've been running some polymer simulations on our cluster and I'm
getting this error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.
What does this error
On 2/25/13 6:09 AM, Group Gro wrote:
Dear Gromacs Users.
I apologize for asking a question that has come up several times by numerous users in the
previous e-mails, but I have read the answers and suggestions to those posts and I am not
still able to solve the problem based on them. It i
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing the list and ask that further comments and
questions will be posted there.
On 2/25/13 7:42 AM, mrda...@gmail.com wrote:
Dear Justin
Greetings
I simulate HIV-1 Protease with its subst
Then, these cosine content's results are all normal?
2013/2/25 Tsjerk Wassenaar
> Because it fits a little bit better to a cosine with full period than
> the first one fits a cosine with half period and the third one fits a
> cosine with 1.5 period.
>
> Tsjerk
>
> On Mon, Feb 25, 2013 at 1:23 PM
Well, the cosine content doesn't tell you very much anyway. And
fitting a cosine with a full period to the second component only makes
sense if the first fits well to a half cosine. If the correlation
coefficient is about .1, it tells you less. It says nothing,
absolutely nothing about convergence
Hi,
Can you update your Gromacs version to an actual release and check if the
problem still occurs. It is very strange that the Einstein-Helfand fit gives
0 for sigma and M_J^2.
Cheers,
Flo
---
Florian Dommert
Dipl. Phys.
Institut für Computerphysik
Universität Stuttgart
Allmandring 3
D-70
Hello,
Thanks.
I will update Gromacs version. Can you tell which version you are using ?
Nilesh
> Hi,
>
> Can you update your Gromacs version to an actual release and check if the
> problem still occurs. It is very strange that the Einstein-Helfand fit
> gives
> 0 for sigma and M_J^2.
>
> Chee
Many Thanks Tsjerk,
It works
A bientot
Stephane
--
Message: 3
Date: Mon, 25 Feb 2013 13:51:53 +0100
From: Tsjerk Wassenaar
Subject: Re: [gmx-users] Building a box pure solvent with genbox for
CG simulations
To: Discussion list for GROMACS users
Messag
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing the list and ask that further comments and
questions will be posted there.
On 2/25/13 9:09 AM, bhavaniprasad vipperla wrote:
Hello sir,
I have been using GROMACS for my MD work. I ha
We are pleased to announce the publication last month of the latest
Gromacs paper:
GROMACS 4.5: a high-throughput and highly parallel open source
molecular simulation toolkit
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson. Pär Bjelkmar,
Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith
Hello,
Thanks for the help. After setting the library path properly, I seem
to be able to get gromacs up and running. However, I have run into another
problem with mdrun and actually running any jobs. When I execute
mdrun -v -deffnm Clp_Test -nt
The output is: Reading file Clp_Test.tpr, V
Dear Gromacs users,
We are pleased to announce the publication last month of the latest
Gromacs paper:
GROMACS 4.5: a high-throughput and highly parallel open source
molecular simulation toolkit
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson. Pär Bjelkmar,
Rossen Apostolov, Michael R. S
Hello dear users,
I just took a look at the new gromacs paper at Bioinformatics, and I
noticed a new tool g_bar, which is used for free energy calculations. I
also found a nice tutorial by Justin Lemkul. While I'm adapting the
workflow to my system, I'd like to know from anyone with more exper
My personal opinion is that for large protein-protein calculations,
the free energy should be computed through potential of mean force
calculations, NOT alchemical methods, using the endpoints (properly
corrected) to determine the free energy of association.
There are a number of tutorials and exa
Hi, all gmx-users,
I am trying to simulate a system of an ion restrained at the center of
water cluster. So I set pbc = no, used "cut-off" for coulomb and vdw. To
restrain the ion at the center of water cluster, I used COMM-pulling. Set
water molecules and the ion in two groups, and applied dista
That's strange, it seems that mdrun gets stuck somewhere. This should not
happen, but as we don't actively test cygwin, we can't be sure what's
happening. It would be great if you could help us figure out what is going
wrong.
Could you try doing the following:
- run with -ntmpi 1 -ntomp 1 (i.e sin
Hi,
I have run the 3 scenarios that you mentioned. The commands and output
are pasted below.
Thanks,
Mike
***Trial 1***
mdrun -v -deffnm Clp_Test -ntmpi 1 -ntomp 1
Reading file Clp_Test.tpr, VERSION 4.6 (single precision)
Using 1 MPI thread
Can not set thread affinities on the current pl
Hi,
Just need some advice regarding the following results I obtained while
following the tutorial from this site, using a protein structure that I
modelled using Modeller.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
1. My output plot of RMSD doesn't converge.
On 2/25/13 9:38 PM, Ewaru wrote:
Hi,
Just need some advice regarding the following results I obtained while
following the tutorial from this site, using a protein structure that I
modelled using Modeller.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
1. My
Dear Justin,
Oh, no wonder. Thank you so much for your prompt reply! :)
Best wishes.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5005885.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Sir,
I have tried Berendsen barostat for Pcoupl. Still I get the same error.
Thank you,
regards,
Anu
On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul wrote:
>
>
> On 2/25/13 12:16 AM, Anu Chandran wrote:
>
>> Dear users,
>> I am trying to do a coarse grained simulation of an octamer of a 350
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