Dear users,
I want to run TPI of water in a binary mixture of water DMSO system. My
question is, how to add the extra water or extra DMSO molecule, or
precisely, how to get the NEW set of coordinates for one water OR one DMSO
molecule?
I will appreciate your reply.
Rikg
--
View this message
Hi,
I'm doing the protein insertion into the lipid membrane. After shrinking for 30
times, I visualized the system, but the secondary structure of protein is still
incomplete . How come? I finished the InflateGRO step.
Thanks for your suggestions in advance.
Sincerely,
Shima
--
gmx-users
Dear Tsjerk,
I am very thankful to you for your reply and sorry
for delay as it has taken much time to understand the things properly.
I have gone through the material that you have attached with this mail that
is really useful.
Now I have understood that large change in
Thank you,
At the end the problem was solved just increasing the time
coupling constant of the barostat tau_p. The original
value of 0.15 that I set at the beginning was too small,
with 0.5 works fine.
On Tue, 09 Oct 2012 14:05:43 -0400
Justin Lemkul jalem...@vt.edu wrote:
On 10/9/12
Hi Ramesh,
You already got a good handle on it! You can subtract and add vectors
without changing the lattice. Now, the box in gromacs will be
something like ((ax, 0, 0), (bx,by,0),(cx,cy,cz)). If cx 0.5*ax,
then you can change the vector to (cx-ax,cy-0,cz-0), and the new |cx'|
will always be
Thank you,
At the end the problem was solved just increasing the time coupling constant
of the barostat tau_p. The original value of 0.15 that I set at the
beginning was too small, with 0.5 works fine.
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View this message in context:
Martini FF cannot model changes in secondary structure ... other CG FF
can. You'll find them easily in the literature. Notably the ones from
Deserno or Derreumaux.
On Oct 10, 2012, at 2:03 PM, rama david wrote:
Hi friends,
I planed to use the martini force-field for my simulation study
Thank you for your reply,
Are these Cg can be used in Gromacs.
Thank you in advance.
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote:
Martini FF cannot model changes in secondary structure ... other CG FF
can. You'll find
Nope, but on other softwares.
On Oct 10, 2012, at 2:50 PM, rama david wrote:
Thank you for your reply,
Are these Cg can be used in Gromacs.
Thank you in advance.
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl
wrote:
Martini
Hi thank you
Please told me the name of Freely available software on which these FF can
be used ..
Thank you in advance
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:26 PM, XAvier Periole x.peri...@rug.nl wrote:
Nope, but on other softwares.
On Oct 10, 2012, at
Hi rama,
actually MARTINI has been further improved to allow secondary structure
change.
The title is:
*Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model:
Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides*
and here there is a link to the paper:
No, it does NOT!
HAve you red the paper?!
This implementation is an adoc representation to mimic specific
sequences of short peptides! They do never for any secondary structure!
On Oct 10, 2012, at 3:05 PM, francesco oteri wrote:
Hi rama,
actually MARTINI has been further improved to
On 10/10/12 5:43 AM, Shima Arasteh wrote:
Hi,
I'm doing the protein insertion into the lipid membrane. After shrinking for 30
times, I visualized the system, but the secondary structure of protein is still
incomplete . How come? I finished the InflateGRO step.
Visualization oddities
What, precisely, do you mean the SS of the protein is still incomplete? When
you use inflategro, the conformation of your
protein is intended to remain as in your initial conformation. Did you forget
to use position restraints
on your protein during the contraction steps (
How can there be forces for holonomic constraints? Is this described by an
equation in the manual?
Just because there are values in the pullf.xvg file does not mean that these
values are forces.
If they are forces, what is the force constant and what is the equation that
defines this force?
I exactly followed the steps in Justin's tutorial of KALP15-DPPC, so I applied
position restrain to restrain the protein in the step before iteration.
It doesn't seem to be artifact, because when I select only the protein in VMD,
I see a broken secondary structure.
Sometime ago, other gmx
Can you compute the Ca RMSD to the starting structure (using structural
fitting) as a function of inflategro step
and post it somewhere online and link it here? It is very difficult to know
what is going on based simply on the
fact that VMD doesn't render your protein as you expect it to.
Sounds like you ran out of memory. Many clusters have a few large-memory nodes.
Can you use one of those?
It's failing on a call for 1.3 Gb of memory, which by itself isn't really a
lot...
Also, can you confirm 250 A box length, not 250 nm box length? Gromacs defines
length in units of nm.
Thanks..You are right...The last line of gro file says 250 so it is in nm!...
On 10 October 2012 12:30, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Sounds like you ran out of memory. Many clusters have a few large-memory
nodes. Can you use one of those?
It's failing on a call for
So perhaps you don't need a box this big?
a box length of 25 nm might be within your available memory. Otherwise, talk to
your cluster's sysadmins.
I am not sure that you're going to get any useful statistics on a box of length
250 nm in any event. A box that size will fit about 1 billion
Update:
Ladasky wrote
Justin Lemkul wrote
Random segmentation faults are really hard to debug. Can you resume the
run
using a checkpoint file? That would suggest maybe an MPI problem or
something
else external to Gromacs. Without a reproducible system and a debugging
backtrace,
On 10/10/12 1:33 PM, Ladasky wrote:
Update:
Ladasky wrote
Justin Lemkul wrote
Random segmentation faults are really hard to debug. Can you resume the
run
using a checkpoint file? That would suggest maybe an MPI problem or
something
else external to Gromacs. Without a reproducible
Hi again,
The reason I have this big box is that I have fully extended chains of
the length of ~ 250 nm,. In fact this 250 nm is the minimum size that
I can fit the chain in the box; and I am going to fill this box with
solvent and use NPT to increase the density. So I dont need to fill up
the
On 10/10/12 4:24 PM, Juliette N. wrote:
Hi again,
The reason I have this big box is that I have fully extended chains of
the length of ~ 250 nm,. In fact this 250 nm is the minimum size that
I can fit the chain in the box; and I am going to fill this box with
solvent and use NPT to increase
On Wed, Oct 10, 2012 at 10:24 PM, Juliette N. joojoojo...@gmail.com wrote:
Hi again,
The reason I have this big box is that I have fully extended chains of
the length of ~ 250 nm,. In fact this 250 nm is the minimum size that
I can fit the chain in the box; and I am going to fill this box
By the way, if you place your solvent molecule (-cs .gro) into a
very large box, such as 10x10x10nm, genbox may perform well. I did NOT
try, just an idea.
For the overall system setup, I would rather follow the previous
comments anyway.
On Wed, Oct 10, 2012 at 10:49 PM, Dr. Vitaly Chaban
Hi friends,
I'm interested in using Thole type model for water (polarizable) TTM2
J. Phys. Chem. A, 2006, 110 (11), pp 4100 or TTM3 ;J. Chem. Phys. 128,
074506 (2008) ) model.
Can someone send me itp file for water..
Thanks
Ananya
--
gmx-users mailing listgmx-users@gromacs.org
Hi,
I will try to compress before doing genbox. As for the number of atoms, as
I said I *dont *intend to fill up the whole box with solvent. So I put
around 4000 solvent molecules to get the desired polymer Wt%, hence there
would be a lot of free space for a total of 120 000 atoms approx..Also I
Dear all,
Is the form of the .n2t file (read by x2top to produce the top file) the same
for all forcefields? I am using the CHARMM forcefield but I could not find an
ffcharmm27.n2t file.
Regards
Elie --
gmx-users mailing listgmx-users@gromacs.org
On 10/10/12 10:35 PM, Elie M wrote:
Dear all,
Is the form of the .n2t file (read by x2top to produce the top file) the same
for all forcefields? I am using the CHARMM forcefield but I could not find an
ffcharmm27.n2t file.
The .n2t format is universal. Most force fields do not have .n2t
Ok. This means that I have to form the .n2t file for the CHARMM field as it is
required by x2top. For the OPLSAA field the format was:
Copls_1570.000 12.011 4H 0.108 H 0.108 H 0.108 C 0.150C
opls_1580.000 12.0114H 0.108 H 0.108 C 0.150 C
On 10/10/12 11:11 PM, Elie M wrote:
Ok. This means that I have to form the .n2t file for the CHARMM field as it is
required by x2top. For the OPLSAA field the format was:
Copls_1570.00012.011 4H 0.108 H 0.108 H 0.108 C 0.150C
opls_1580.000 12.0114H
Understandable. I meant the content of the .n2t file itself ; will it contain
the same info as the OPLSAA with just changes in values according to the CHARMM
field?
Thank you
Elie
Date: Wed, 10 Oct 2012 23:13:34 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users]
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