Dear Justin,
Based on your questions to my simulation, I posted here yesterday hopefully it
was the correct way to reply in this forum.
In this morning I got a list of new windows of umbrella sampling, the overlap
is sufficient enough, but I saw another problem: In the histogram figure, the
Yes, it could be possible. You have to install it on your local folder
where you have the right permissions. This is specified with the
--prefix option on the configure script (if using automake/automake
installation) or the corresponding option with cmake (I don't know wich
one is it, check
A good place to start your reading:
http://www.gromacs.org/Documentation/Installation_Instructions
Javier
El 22/05/12 11:48, Shima Arasteh escribió:
Would you guide me to a link which may help me?
Thanks so much.
Sincerely,
Shima
Hi Justin, your suggestion got close. However, let me give an example. You
can use the Gly-Gly-Gly example I am attaching and do this:
pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none
/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp aGGGp.top
if you look
Hi, all,
I try to use g_sorient program to analyze SPC water molecules orientation
around atomic ion. As I understand two molecule vectors are analyzed. For
theta_1 calculation the dipole moment direction is used. Other two orthogonal
vectors may be analyzed through theta_2 depending on -v23
Hi,
have a look at out recently developed all-atom force field.
It is compatible with AMBER force fields for proteins (ff99SB, ff99SB-ILDN and
ff03).
The compatibility was tested via microsecond simulations of a peptide embedded
in a bilayer. The paper describing the peptide simulations
Dear all gromas users,
While i am running the grompp after first
mdrun command i got the following error.
File input/output error:
pr.mdp
Is there any explanation why is this happening?
I would appreciate any help.I am new in using MD and gromacs in particular.
On 5/22/12 1:26 PM, Seera Suryanarayana wrote:
Dear all gromas users,
While i am running the grompp after first
mdrun command i got the following error.
File input/output error:
pr.mdp
Is there any explanation why is this happening?
It means that file
On 5/22/12 12:46 PM, Alan wrote:
Hi Justin, your suggestion got close. However, let me give an example. You can
use the Gly-Gly-Gly example I am attaching and do this:
pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none
/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o
On 5/22/12 9:36 AM, Du Jiangfeng (BIOCH) wrote:
Dear Justin,
Based on your questions to my simulation, I posted here yesterday hopefully
it was the correct way to reply in this forum.
You've still replied to the entire digest message (which I've cut out); please
make sure to keep replies
Dear all gromas users,
While i am running the grompp -c 1UZ9_em.gro -p 1UZ9.top -o
1UZ9_b4pr.tpr -f pr.mdp after first mdrun command i got the following error.
File input/output error:
pr.mdp
Is there any explanation why is this happening?
I would appreciate any help.I am new in using MD
On 5/22/12 2:00 PM, Seera Suryanarayana wrote:
Dear all gromas users,
While i am running the grompp -c 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f
pr.mdp after first mdrun command i got the following error.
File input/output error:
pr.mdp
Is there any explanation why is this happening?
Hi Joakim,
I am interested to know what other lipids this force field has been
extended to include. Do you have parameters for unsaturated lipid tails
and other classes of phospholipid (such as PE and PG)?
Cheers
Tom
Joakim Jämbeck wrote:
Hi,
have a look at out recently developed
Hi Justin,
As for the maximum of 0.4 nm fluctuation of my pulled protein, I used g_dist to
calculate the distance between my pulled protein and stable part in a window,
where the distance is treated as the fluctuation of the protein along z-axis.
Well, from pullx.xvg, the position moved a lot
Hi Tom,
we have parameters for unsaturated tails now as well as for PE lipids ready for
use, the manuscript for these have been submitted.
PG and PS lipids are on the way and parameters for cholesterol and
sphingomyelin are finished now and the manuscript should be finished relatively
soon.
Think it would be best to show the .mdp file, else we can only guess
what the parameters are.
From the histogram it looks like that the force constant of the
restraining potential is too low, since the histograms are really wide,
but pull_k1=1000 is a 'normal' value.
On thing which confueses me
Thanks Joakim,
I will be very interested to see how these different lipids behave. This
looks like it could be a really useful force field. We have also
developed some parameters for PE, PG and Cardiolipin lipids which you
might want to have a look at (for comparison with your ongoing
Is this FF available for others to use?
Thanks.
Sincerely,
Shima
From: Thomas Piggot t.pig...@soton.ac.uk
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, May 22, 2012 7:39 PM
Subject: Re: [gmx-users] forcefields for lipids
Hi,
-s before -deffnm works, now after starting once more REMD from
the scratch I can do restart.
Thanks.
Best
tomek
On Mon, May 21, 2012 at 2:39 AM, mu xiaojia muxiaojia2...@gmail.com wrote:
try put -s before -deffnm
mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append
On
Thank you for your reply, Thomas. Under your explanation, I am well understood
of the terms: pull_k and pull_rate.
Here I upload both md_umbrella.mdp and md_pulling.mdp.
I have to mention that it is coarse gained system with Martini force field.
At the same time, i am going to run a simulation
*.mdp files.
Jiangfeng.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands
md_umbrella.mdp
Description: md_umbrella.mdp
try trjconv, maybe your reference gro/tpr file is cubic?
make sure:
trjconv -s the_dodecahedral_generated.tpr -f the_dodecahedral_generated.gro
-o your_aim.pdb
On Tue, May 22, 2012 at 9:27 AM, patrick wintrode pat_w...@yahoo.comwrote:
After generating my protein .gro and .top files and doing
Dear gromacs users,
I am trying to run free energy calculation using the CHARMM force-field.
I am able to generate the .top file, but when I try to obtain the .tpr,
grompp gives the following error:
ERROR 1 [file rest2.top, line 11420]:
Cannot automatically perturb a torsion with multiple
The ZINC database page and the NIH PubChem one can help you in that.
Best regards
Lucio
El sáb, 19-05-2012 a las 18:10 -0700, Nancy escribió:
Hi All,
Does anyone know of a free cheminformatic service from which it's
possible to narrow down a search for molecules by inputting limits on
their
I never worked with the MARTINI (or other coarse-grained) force field,
but this in the umbrella.mdp
title = Umbrella pulling simulation
integrator = md
dt = 0.019
looks suspicious. The dt is about an order of magnitude greater than one
uses in normal (bond-)constrainted
On 5/22/12 6:53 PM, Thomas Schlesier wrote:
I never worked with the MARTINI (or other coarse-grained) force field, but this
in the umbrella.mdp
title = Umbrella pulling simulation
integrator = md
dt = 0.019
looks suspicious. The dt is about an order of magnitude greater than one uses in
On 5/22/12 6:36 PM, mu xiaojia wrote:
try trjconv, maybe your reference gro/tpr file is cubic?
make sure:
trjconv -s the_dodecahedral_generated.tpr -f the_dodecahedral_generated.gro -o
your_aim.pdb
The triclinic representation is used for all boxes in Gromacs as it is the most
compact.
Hi Shima,
Yes, the phospholipid parameters are available to use. I am currently in
the process of uploading them to the Lipidbook website. If you check
this website soon they should be available to download (DPPE and POPE
parameters and bilayers are already there). For accessing them on
I'm going to simulate the protein in POPC bilayer. Do you suggest this
forcefield for this kind of bilayer too?
Thanks so much for your reply.
Sincerely,
Shima
From: Thomas Piggot t.pig...@soton.ac.uk
To: Discussion list for GROMACS users
Hi,
In my opinion the choice of force field will depend upon exactly what
you are simulating and why you are simulating it. Different force fields
(both lipid and protein) have their own advantages and disadvantages and
so it is really up to you to decide this (after doing some background
Hello
I am trying to change a crystal structure(wih amc or cif format) into a
.pdb format; but gromacs gives me input/output error; which means my input
file has the wrong format. Do u have any suggestions how to convert or what
software to use?
Regards.
--
gmx-users mailing list
All:
I know this question isn't particularly related to GROMACS, but I've contacted
the PRODRG admin in the past have never received a response. That said, is
anyone experiencing technical issues acquiring a token to use PRODRG after
entering an email address?
Hi all,
My pdb file contains only c-alpha atoms , i have named alternate
CA atoms(res) as CB(1res CA,2res CB,3res CA...) , I have given my residue
name as ALB, accordingly i have changed .rtp ,atomtype
files,residuetype.dat. i want to use force field(charmm27.ff) present in
current
Dear all,
I am attempting to keep a Zn ion in place in a zinc finger motif using
distance restraints to the coordinating cysteine residues. The zinc is
structural and not catalytic, and it was suggested from this list that
using distance restraints should suffice without the need for
On 5/22/12 8:49 PM, rainy908 wrote:
All:
I know this question isn't particularly related to GROMACS, but I've contacted
the PRODRG admin in the past have never received a response. That said, is
anyone experiencing technical issues acquiring a token to use PRODRG after
entering an email
On 5/22/12 9:24 PM, mohan maruthi sena wrote:
Hi all,
My pdb file contains only c-alpha atoms , i have named alternate CA
atoms(res) as CB(1res CA,2res CB,3res CA...) , I have given my residue name as
ALB, accordingly i have changed .rtp ,atomtype files,residuetype.dat. i want to
On 5/22/12 9:25 PM, Thomas Grant wrote:
Dear all,
I am attempting to keep a Zn ion in place in a zinc finger motif using distance
restraints to the coordinating cysteine residues. The zinc is structural and
not catalytic, and it was suggested from this list that using distance
restraints
Greetings all,
I now realise I asked too many questions with that one post.
I would like to check that mdrun -rerun can be used to do single point energy
calculations on the co-ordinate frames from my trajectory using a different
electrostatic model by changing the .mdp file used by grompp to
Hello community,
I'm just trying to explore what kind of calculations one can do on
polymer systems (pure or in water) in order to validate the force
field works accurately for that system. I know there are basics such
as density, volume, dH of vaporization, isothermal compressibility,
heat
On 23/05/2012 1:24 AM, Tomek Wlodarski wrote:
Hi,
-s before -deffnm works, now after starting once more REMD from
the scratch I can do restart.
I use
mpirun mdrun_mpi -multi $nrepls -deffnm ${name}_sim $npme -cpi
${name}_sim -append
and it Just Works with 4.5.5.
Mark
Thanks.
Best
On 23/05/2012 8:36 AM, Tom Dupree wrote:
Greetings all,
I now realise I asked too many questions with that one post.
I would like to check that mdrun -rerun can be used to do single point energy
calculations on the co-ordinate frames from my trajectory using a different
electrostatic model by
On 23/05/2012 4:20 AM, Muyi Xu wrote:
Hello
I am trying to change a crystal structure(wih amc or cif format) into
a .pdb format; but gromacs gives me input/output error; which means my
input file has the wrong format. Do u have any suggestions how to
convert or what software to use?
Perhaps
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