Greetings
I'm studying protein unfolding by CTMD and REMD simulations to capture the
intermediate states.
I want to calculate the non-native contacts formed during the intermediate
state.
Suggestions please
Thanks
Suhani
Proteomics and Structural biology Lab
CSIR-IGIB
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Dear gmx-users,
Thanks for the nice reply.
I have corrected the pull code as:
; Pull code
pull= umbrella
pull_geometry = position ;
pull_dim= N N Y
pull_start = yes; define initial COM distance > 0
pull_ngroups= 2
pull_group0 = cbilayer ; center of
I'd imagine using constraint type 2 between suitable virtual sites would be
a much better approach. Not sure it actually works, though!
Mark
On Tue, Jan 14, 2014 at 8:01 PM, Yuan Hu wrote:
> Dear Gromacs user/developer,
>
>
> I want to modify the Shake program in gromacs 4.x to constrain the
On 1/14/14, 3:34 PM, decaiyu wrote:
Dear All,
When I look at the dihedral angle definition (see below) for gromos43a1
force field, most equilibrium angles are either 180 or 0 degrees.
I assume that the second number represent the strength of dihedral angle
term and the third one is the power.
On 1/14/14, 2:13 PM, paulxie wrote:
Justin Lemkul wrote
You will have to position the protein differently if it is oriented
asymmetrically with respect the the membrane. The same principles apply,
but
box vectors will certainly be different, as will the editconf command.
-Justin
-
https://
Dear All,
When I look at the dihedral angle definition (see below) for gromos43a1
force field, most equilibrium angles are either 180 or 0 degrees.
I assume that the second number represent the strength of dihedral angle
term and the third one is the power.
How do I define the gd term involving a
Hi All,
I would like to do an analysis of water's properties near PC/PG headgroups
compared to those of bulk water. One useful property I can think of is 2D
sliced RDF, i.e., the lateral radial distribution function of water in a
thin layer, or say, dividing a thick slab of water into thin layers
Justin Lemkul wrote
>
> You will have to position the protein differently if it is oriented
> asymmetrically with respect the the membrane. The same principles apply,
> but
> box vectors will certainly be different, as will the editconf command.
>
> -Justin
>
> -
> https://maillist.sys.kth.se
Dear Gromacs user/developer,
I want to modify the Shake program in gromacs 4.x to constrain the reaction
coordinate to a fixed value, and then get the corresponding constrain force
applied.
Does anyone could help me about which file i need modify, and how to modify it?
Any help will be appre
Lindemann criterion might be easier. See For example,
* Materials science: Melting from within
Nature 413, 582-583 (11 October 2001) | doi:10.1038/35098169
Robert W. Cahn
On 14 January 2014 15:35, Golshan Hejazi wrote:
> Hello everyone!
>
> I would like to compute the melting point of a drug c
On 1/14/14, 12:37 PM, Albert wrote:
Hello:
I found a problem of lipids name when I use editconf each time. My lipids name
are: POPC and POPG. When I run command:
editconf -f em.gro -o em.pdb
the name of my lipids for both POPC and POPG are "POP". I am just wondering how
can we solve this pro
I think you can't. People have asked similar questions before. You need to
rename the lipids yourself to 3 letter names e.g. POC and POG.
> Hello:
>
> I found a problem of lipids name when I use editconf each time. My
> lipids name are: POPC and POPG. When I run command:
>
> editconf -f em.gro -o
Hello:
I found a problem of lipids name when I use editconf each time. My
lipids name are: POPC and POPG. When I run command:
editconf -f em.gro -o em.pdb
the name of my lipids for both POPC and POPG are "POP". I am just
wondering how can we solve this problem by exporting the full name of
I would just like to also re-iterate the point made by Justin. The
conversion of the lipid parameters into GROMACS format was done before
there were published updates to other parts of the CHARMM force field
and so it is only the lipids which are the CHARMM36 parameters.
Regarding the choice o
On 1/14/14, 11:38 AM, Albert wrote:
It is good to know that the c36 and CGenFF is actively update. I just noticed
that this new version c36 no longer contains classic TII3P water models:
1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
2: TIP4P TIP 4-point
It is good to know that the c36 and CGenFF is actively update. I just
noticed that this new version c36 no longer contains classic TII3P water
models:
1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with
LJ on H
2: TIP4P TIP 4-point
3: TIP5P TIP 5-point
4: SPC sim
Google knows about two GROMACS REMD tutorials, by the way!
Mark
On Tue, Jan 14, 2014 at 1:30 PM, vidhya sankar wrote:
> Dear Justin Thank you For your previous reply
>
> I would like to do REMD (Replica exchange MD) in gromacs I am very happy if
> you paste tutorial for REMD, Targeted MD , Con
On 1/14/14, 10:58 AM, hubert santuz wrote:
I use this charmm36
(http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from
Piggot et al, 2012, JCTC) which have slight differences in the order and in the
name of few atoms compared to the one you used.
So, everything I said conce
I use this charmm36
(http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz,
from Piggot et al, 2012, JCTC) which have slight differences in the
order and in the name of few atoms compared to the one you used.
So, everything I said concern only this version ;)
Cheers,
Hubert
Le
Hi,
Check your position restraints defined in the itp/top file for the lipid
molecules and if they correctly reflect the keywords in the MDP file.
One reason for the second warning might be that the order of appearance of
your lipids and other atoms is not the same between the top and the
PDB/GRO
On 01/14/2014 04:12 PM, Justin Lemkul wrote:
The .top is what matters, and your topology showed a clearly different
order of atoms. Check the correspondence of the output configuration
from pdb2gmx and the .top file. Inputs and .rtp entries are
irrelevant once pdb2gmx is done working.
-Just
Justin,
Thanks for your reply to this and my previous post!
I looked at my .mdp and found the following line actually restrict the atom
positions.
; VARIOUS PREPROCESSING OPTIONS
define = -DPOSRES
I have another question on dihedral angle parameter definition. I will post
in a separate message.
I
On 1/14/14, 10:09 AM, Albert wrote:
Hi Justin and Hubert:
Many thanks for your kind pointing out. Are you using the new version of
CHARMM36? I am using the one from here:
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36_gmx_format_sep13.tgz
I opened the m
Hi Justin and Hubert:
Many thanks for your kind pointing out. Are you using the new version of
CHARMM36? I am using the one from here:
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36_gmx_format_sep13.tgz
I opened the merged.rtp file within the charmm36.ff
Hello everyone!
I would like to compute the melting point of a drug crystalline system. In the
literature, there exist a good number of methods to do so!
Among them, I read Gibbs-Duhem integration technique in which one needs to
provide a reference coexistence of solid/liquid. I read some artic
Hi,
I just came across this issue a few days ago (with charmm-gui also).
In fact, atoms C13, C14 and C15 should be just after the C12 atoms in
the pdb (to match the itp file).
Here a piece of code that I used to retrieve the good order for all POPC
molecules in your gro file (on unix platform
On 1/14/14, 8:07 AM, 李晴 wrote:
Dear gmx-users,
I use GMX to simulate a protein 700 peptide long with a ligand. The
protein-ligand complex is put in a box with explicit water. I use AMBER99 force
field.
The epsilon-r was set with the default value 1, with coulombtype=PME. The
problem is, the
On 1/13/14, 7:40 PM, Rini Gupta wrote:
Dear gmx-users,
I want to calculate Potential of Mean Force (PMF) of a lipid in a bilayer
by umbrella sampling method using coarse grain molecular dynamics
simulations. My simulation system consists of
76 (PEPC and GDPE lipids mixture), 2495 water molecul
On 1/14/14, 6:41 AM, Albert wrote:
Hello:
I am trying to equilibrate a membrane system which contains both POPC and POPG.
I generate the system with charmm-gui, and I try to minimize it in Gromacs. Here
is my em.mdp file:
define = -DPOSRES_POPC -DPOSRES_POPG
constraints = none
integ
Dear gmx-users,
I use GMX to simulate a protein 700 peptide long with a ligand. The
protein-ligand complex is put in a box with explicit water. I use AMBER99 force
field.
The epsilon-r was set with the default value 1, with coulombtype=PME. The
problem is, the energy generated from .xtc file usi
On 1/14/14, 7:29 AM, vidhya sankar wrote:
Dear Justin Thank you For your previous reply
I would like to do REMD (Replica exchange MD) in gromacs I am very happy
if you paste tutorial for REMD, Targeted MD
Dear Justin Thank you For your previous reply
I would like to do REMD (Replica exchange MD) in gromacs I am very happy
if you paste tutorial for REMD, Targeted MD , Constraint MD and Non
Equilibrium MD
as
Dear Justin Thank you For your previous reply
I would like to do REMD (Replica exchange MD) in gromacs I am very happy
if you paste tutorial for REMD, Targeted MD , Constraint MD and Non
Equilibrium MD
as
Hello:
I am trying to equilibrate a membrane system which contains both POPC
and POPG. I generate the system with charmm-gui, and I try to minimize
it in Gromacs. Here is my em.mdp file:
define = -DPOSRES_POPC -DPOSRES_POPG
constraints = none
integrator = steep
dt = 0.00
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