Hi,
Check this article:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131
HTH Balazs
Quoting simula_460 bharat.85.m...@gmail.com:
Hi,
I tried again simulating the same peptide with OPLS FF for 2000 ns time
duration. I used VMD for the secondary structure analysis and
Thanks for the message, I have a .pdb containing my membrane protein
inside the leaflet of popc bilayer, so i wanted to remove the
interacting lipid molecules, hence i used inflategro.
I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce
a protein bilayer system using that,
Hi everybody,
I want to use pdb2gmx for my protein.
My protein has a ACE cap at one termini. And I looked it up in the
aminoacids.rtp file and there is also a ACE entry.
But still I get an error when using pdb2gmx
my command is like this:
pdb2gmx -f 3m71_hyd_cap.pdb -o 3m71.gro -p 3m71.top
On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote:
Thanks for the message, I have a .pdb containing my membrane protein
inside the leaflet of popc bilayer, so i wanted to remove the
interacting lipid molecules, hence i used inflategro.
I used CHARMM GUI only to produce a pure POPC
On 18/07/2012 7:58 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to use pdb2gmx for my protein.
My protein has a ACE cap at one termini. And I looked it up in the
aminoacids.rtp file and there is also a ACE entry.
But still I get an error when using pdb2gmx
my
On 7/18/12 5:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to use pdb2gmx for my protein.
My protein has a ACE cap at one termini. And I looked it up in the
aminoacids.rtp file and there is also a ACE entry.
But still I get an error when using pdb2gmx
my
On 7/18/12 3:03 AM, joja...@jgypk.u-szeged.hu wrote:
Hi,
Check this article:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131
HTH Balazs
In addition, it is important to realize that a single trajectory represents one
possible outcome, and no matter how long it is,
Dear gmx users,
I am running a QM/MM optimization using the interface with Orca and the
bOPT=Yes option. I departed from a snapshot taken from a MM molecular
dynamics simulation. The calculation starts running well, and the QM part
converges successfully after 29 optimization cycles. However, at
Hi All,
I would like to compute the time correlation function (tcf) of the
C-H bond vector for all the C-H bonds on the hydrocarbon chain of
surfactants in two micelles simulated with the CHARMM and gromos54A7
force fields. It is not clear to me how do that.
Below what i did
1- For the
no, water problem is solved, but my protein is still out of the bilayer,
When i change:minimize my box vector values and inflate...the protein
is packed inside. but now the area per lipid is too low for popc its
like 0.148 nm2
On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul jalem...@vt.edu
On 7/18/12 7:07 AM, Manikam Sadasivam Saravanan wrote:
no, water problem is solved, but my protein is still out of the bilayer,
When i change:minimize my box vector values and inflate...the protein
What does this mean?
is packed inside. but now the area per lipid is too low for popc its
Dear Gromacs Users!
I have two trajectories with removed PBC which was done by the below command.
trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc
mol -ur compact
Both of that trajectories are of the same system- when one trajectory
have been manyally stoped I've run the
On 7/18/12 7:35 AM, James Starlight wrote:
Dear Gromacs Users!
I have two trajectories with removed PBC which was done by the below command.
trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc
mol -ur compact
Both of that trajectories are of the same system- when one
my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC
14 system_inflated.gro 5 area.dat
my gro file looks like,
membrane protein in POPC 121-310KWITNOIONS
59522
1SER N1 -2.092 -1.832 -1.359
1SERHT12 -2.149 -1.861 -1.436
1SERHT23 -2.150
On 7/18/12 7:48 AM, Manikam Sadasivam Saravanan wrote:
my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC
14 system_inflated.gro 5 area.dat
my gro file looks like,
membrane protein in POPC 121-310KWITNOIONS
59522
1SER N1 -2.092 -1.832 -1.359
1SER
Dear users,
I am getting the problem in reading full .xtc file. The simulation time is 200
ns. But while giving command
./g_hbond -f dna_pro_whole_nojump_cent.xtc -s sys2.tpr -num Pro_H2A2.xvg
I am getting below error. The .xtc file is reading only till 20ns and givng
error. I am not
On 7/18/12 8:24 AM, nikhil gadewal wrote:
Dear users,
I am getting the problem in reading full .xtc file. The simulation time is 200
ns. But while giving command
./g_hbond -f dna_pro_whole_nojump_cent.xtc -s sys2.tpr -num Pro_H2A2.xvg
I am getting below error. The .xtc file is reading
Hi Gromacs friends
I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
Surface tension coupling work with only Berendsen Press coupling.
Please , would you tell me how to calculate lateral surface tension from
P|| ( lateral press ) and Pz( Perpendicular press ) ???
( Why to
Justin
thanks for advise
I've used the bellow command for both trajectory
trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc
but resulted merged_noPBC.xtc consist of data from only second
trajectory although in the log file both trajectories have been
processed
File
On 7/18/12 9:34 AM, James Starlight wrote:
Justin
thanks for advise
I've used the bellow command for both trajectory
trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc
but resulted merged_noPBC.xtc consist of data from only second
trajectory although in the log file both
Justin thanks,
Works perfect.
James
2012/7/18 Justin Lemkul jalem...@vt.edu:
On 7/18/12 9:34 AM, James Starlight wrote:
Justin
thanks for advise
I've used the bellow command for both trajectory
trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc
but resulted
Hi Gromacs Friends,
I completed the Justin Protein KALP - lipid tutorial ...
I want to simulate the DPPC lipid bilayer membrane under
Stress condition ( Lateral tension = 20 mNm/m)..
For stress condition I made the following npt.mdp
; Temperature coupling is on
tcoupl =
Dear All,
A quick question, here
g_angle with the -oc word can compute the dihedral correlation function C(t)
as well as g_chi with -corr argument . Do these tools use the same approach
discussed in the paper of van der Spoel and Berendsen 1997 BJ 72 2032.to
compute C(t) ?
Thank you for the
Dear gromacs users,
I am trying to run a replica exchange simulation using the files you find
in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz
The 4 replicas have been generated, as following:
grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp
grompp -p
Hello gromacs users,
I am trying to use pdb2gmx to bring my crystal structure into gromacs
environment. The protein in the crystal has glycosidic linkages. In
charmm, I could attach these carbohydrate structures using PATCH
command.
What is the equivalent of doing this in gromacs?
My initial
On 7/18/12 2:41 PM, kaushik lakkaraju wrote:
Hello gromacs users,
I am trying to use pdb2gmx to bring my crystal structure into gromacs
environment. The protein in the crystal has glycosidic linkages. In
charmm, I could attach these carbohydrate structures using PATCH
command.
What is the
Dear Gromacs users,
I am calculating hydrogen bonds between polymer and water using
Gromacs 4.5.4 and opls-AA force field. Our goal is to extract
coordinates of atoms which form hydrogen bond at each frame.
1. The way I do it now is iterating following commands at every frame
using a script:
On 7/18/12 4:57 PM, zifeng li wrote:
Dear Gromacs users,
I am calculating hydrogen bonds between polymer and water using
Gromacs 4.5.4 and opls-AA force field. Our goal is to extract
coordinates of atoms which form hydrogen bond at each frame.
1. The way I do it now is iterating following
Hi all...
I heard that gromos 54a7 ff is much better for simulations than 53a6. i have
a membrane protein system. To simulate it, should I include the berger lipid
parameters manually as shown in justin Lemkul's membrane protein tutorial?
Thanks
--
View this message in context:
On 7/18/12 5:37 PM, Rajat Desikan wrote:
Hi all...
I heard that gromos 54a7 ff is much better for simulations than 53a6. i have
a membrane protein system. To simulate it, should I include the berger lipid
parameters manually as shown in justin Lemkul's membrane protein tutorial?
The Berger
54A7 also introduced changes to the Gromos96 lipid parameters
How will this change my inclusion of the berger lipid parameters? Any thing
that I should pay special attention to? Are there other lipid parameters
more compatible?
I heard from a faculty member at our Institute that the 53a6 is a bad
On 7/18/12 5:51 PM, Rajat Desikan wrote:
54A7 also introduced changes to the Gromos96 lipid parameters
How will this change my inclusion of the berger lipid parameters? Any thing
that I should pay special attention to? Are there other lipid parameters
more compatible?
There are better force
Thanks for the quick and detailed replies Justin :) This helped clear some
doubts I had.
I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you
referring to?
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999542.html
On 7/18/12 6:13 PM, Rajat Desikan wrote:
Thanks for the quick and detailed replies Justin :) This helped clear some
doubts I had.
I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you
referring to?
CHARMM force fields are largely just sequential additions and
So CHARMM36 would be the best ff for a long membrane protein simulation?
Is it possible to integrate CHARMM36 into Gromacs?
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999544.html
Sent from the GROMACS Users Forum mailing list archive at
I got the answer to whether we can implement CHARMM36 into gromacs...:)
thanks
http://www.gromacs.org/Downloads/User_contributions/Force_fields
I still want your opinion on whether it is the best ff for simulating a
membrane-protein system, and if any modifications to the ff are necessary?
Thanks
Hi,
Justin, I am interested by your comments regarding the CHARMM lipids. In
particular can you elaborate as to why you think that the CHARMM lipids
are better than the united-atom ones (such as Berger and several GROMOS
variants).
As for the original question, the modifications in going
On 7/18/12 6:57 PM, Thomas Piggot wrote:
Hi,
Justin, I am interested by your comments regarding the CHARMM lipids. In
particular can you elaborate as to why you think that the CHARMM lipids are
better than the united-atom ones (such as Berger and several GROMOS variants).
I think there's
Hi,
Yes, I agree with you regarding the combination of Berger and GROMOS
force field and requiring validation. I just wanted to point out the
interactions between the protein and lipid are treated in the same way,
irrespective of the different GROMOS protein force field used (when
using the
On 19/07/2012 12:32 AM, francesco oteri wrote:
Dear gromacs users,
I am trying to run a replica exchange simulation using the files you find
in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz
The 4 replicas have been generated, as following:
grompp -p rest2.top -c 03md.gro -n
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