Hi Alex
You're running just 1ns, which is actually too short for production in
this kind of systems. Enlarge the simulation time (e.g. up to 50ns) and
see if you get a more reasonable Scd plots.
Javier
El 08/11/11 21:40, Alex Jemulin escribió:
Dear Javier
Here is mdp file for MD run
title
Hello,
I am studying the diffusion of a small molecule through a cyclic peptide
based nanotube using pull code, here is my code for pulling,
pull= umbrella
pull_geometry = position
pull_vec1 = 0 0 1
pull_start = yes
pull_ngroups= 1
pull_group0 = Protein
pull_group
Dear gmx Users,
I am wondering what is the value of Number of Contacts (<0.6 nm) between
two groups. When I specify one group - Ligand and second - protein residue
- does it count every dostance within 0.6 nm between every atom from one
group and every atom from the second specified group?
Cheers
Hello users,
I have few conflicting answers from the user mailing list about the
following question.
Using leap-frog integrator, what is the velocity that is WRITTEN in
the trajectory file for a frame corresponding to r(t)? Is it v(t-dt/2)
or v(t). Has the protocol for writing velocity in traject
Dear sir:
this is my BASENAME.ORCAINFO:
! rks b3lyp svp tightscf opt grid4 nofinalgrid
! normalprint
! rijcosx sv/j
*xyz -1 2
S 2.983 3.527 3.279
C 3.007 3.497 3.463
C 3.156 3.478 3.230
C 3.174 3.484 3.088
O 3.236 3.446 3.317
C 3.296 3.455 3.037
C 3.338 3.447 2.901
C 3.473 3.421 2.865
C 3.520 3.4
Hi all,
for a publication i want to list the used OPLS parameters for the
investigated molecules. In GROMACS all atomtypes are uniquely defined by
the atomtype `opls_xyz`. And from the atomtypes one can deduct the
bonded parameters. So it is sufficient to list only the atomtypes and
probably c
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Greeting
After finishing a M.D simulation an ensuring that equilibration of the
protein is done in its solvent cube according to RMS, potential energy
,temperature , pressure , radius of gyration ... etc what structure should
i use for analysis ? is it the average structure of some few last
nanosec
larif sofiene wrote:
Greeting
After finishing a M.D simulation an ensuring that equilibration of the
protein is done in its solvent cube according to RMS, potential energy
,temperature , pressure , radius of gyration ... etc what structure
should i use for analysis ? is it the average struct
Hello
I got the following error (my command is pdb2gmx -f coord.pdb -water tip3p ) :
Warning: Number of atoms in coord.pdb is 0
Software inconsistency error:
Trying to deduce atomnumbers when no pdb information is present
My pdb file has the following structure
HEADER my molecules name
ATO
Looks generally reasonable. Thanks! - Vitaly
On Tue, Nov 8, 2011 at 12:20 PM, Krzysztof Kuczera wrote:
> The ideal gas result is -(1/V)(dV/dp)_T = 1/p , so I suppose the value
> should be = 1.0 bar-1
> under standard conditions
> Krzysztof
>
> On 11/8/11 10:51 AM, Dr. Vitaly V. Chaban wrote:
Lara Bunte wrote:
Hello
I got the following error (my command is pdb2gmx -f coord.pdb -water
tip3p ) :
Warning: Number of atoms in coord.pdb is 0
Software inconsistency error:
Trying to deduce atomnumbers when no pdb information is present
My pdb file has the following structure
HEADER
So would it be reasonable to set rcoulomb = 2 or even 3 nm when rerunning a
trajectory? I am looking at a ligand-antibody system, and I guess the
long-range electrostatic interactions will not be small.
A trick proposed by Nicolas in the mailing list during 2007 is to set
charges to 0.00 for every
I've another question about NMA.
1- As I understood the Sparce matrix method is used on default in case when
my reference structure consist of alot of atoms. If this true the output
Hessian.mtx would be in sparce format, wouldn't it ?
2- How I can convert output.mtx to the txt format ? As the co
Justin,
Could you tell me another alternative ways to replace existing cap groups
in my pdb besides xleap ? ( I've had many problems with the pdb's
processed by this soft). Also I've tried to make topology for the
non-standart caps by PRODRG but I also have some problems with such
parametrisation
James Starlight wrote:
Justin,
Could you tell me another alternative ways to replace existing cap
groups in my pdb besides xleap ? ( I've had many problems with the
pdb's processed by this soft). Also I've tried to make topology for the
non-standart caps by PRODRG but I also have some prob
Please keep the discussion on the list.
Lara Bunte wrote:
Hi
what is wrong in the format or what do I have to change. Please don't
give me a link to the pdb site, I do not understand it :-(
The PDB format requires certain columns with the prescribed information be
present at the specifie
5Hello all,
I am trying to use CHARMM 36 for DPPC membrane simulation. I did the
following so far:
1. Download pdb file containing 128 DPPC molecules from
http://www.charmm-gui.org/?doc=archive&lib=lipid_pure
2. I separated one lipid molecule from the obtained pdb file and used
pdb2gmx -f 1dppc.
On 10/11/2011 12:52 AM, Thomas Schlesier wrote:
Hi all,
for a publication i want to list the used OPLS parameters for the
investigated molecules. In GROMACS all atomtypes are uniquely defined
by the atomtype `opls_xyz`. And from the atomtypes one can deduct the
bonded parameters. So it is suff
On 10/11/2011 6:03 AM, Yun Shi wrote:
So would it be reasonable to set rcoulomb = 2 or even 3 nm when
rerunning a trajectory? I am looking at a ligand-antibody system, and
I guess the long-range electrostatic interactions will not be small.
You can set rcoulomb to anything you like, but there'
On 10/11/2011 6:48 AM, James Starlight wrote:
I've another question about NMA.
1- As I understood the Sparce matrix method is used on default in case
when my reference structure consist of alot of atoms. If this true the
output Hessian.mtx would be in sparce format, wouldn't it ?
2- How I c
Sounds like the ligand is near the edge of the box, so only has to move short
distance then does the jumping you are observing.
The suggestion that has already been make, -pbc nojump, should stop that.
Another option is to center the box on a residue within the protein which is
near the spot at
Hello everyone,
I am using g_mindist with -pi option to look at the minimal distance
between periodic images of my protein-ligand system.
It appears that after a certain amount of time (12 ns or 30 ns or ...),
there would be a sudden drop of min distance from well above 2 nm to around
0.15 nm.
I
Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm,
the min periodic image dist still dropped abruptly to 0.172 or something
like this after around 35 ns or 30 ns (different trajectory with same
topology).
So I wonder if this is just inevitable and we should live with it?
Th
Dear Sir:
How to write a correct BASENAME.ORCAINFO file? According to the instruction
“In the ORCAINFO-file the method, basis set and all other ORCA-specific
keywords must be given.” It means that BASENAME.ORCAINFO may not contain
coordinates of QMatoms part, but when groamcs-ORCA runs , it
Hi,
this is currently not possible. Currently you can only do temperature or
Hamiltonian RepEx. As far as I know 4.6 will support both simultaneous. In
the mean time you might be able to accomplish your goal
by reformulating the Temp-RepEx as a Hamiltonian RepEx as is done in the
newer version of
Hi,
for Hamiltonian RepEx you need to formulate the different states as a
function of lambda. Look at the free energy documentation to see how to
describe different tables for different lambdas.
Roland
2011/11/8 杜波 <2008d...@gmail.com>
> dear teacher,
>
> if i want to do remd with different
Hi Yun,
Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before
using g_mindist.
Also visually check a frame that is reported to have closed contacts.
Hope it helps,
Tsjerk
On Nov 10, 2011 1:45 AM, "Yun Shi" wrote:
Sorry, I just found that even if I use a dodecahedron box w
On 9/11/2011 9:09 PM, Steven Neumann wrote:
Dear gmx Users,
I am wondering what is the value of Number of Contacts (<0.6 nm)
between two groups. When I specify one group - Ligand and second
- protein residue - does it count every dostance within 0.6 nm between
every atom from one group and eve
Thank you, Mark.
By the way, also I have some question about data analysing
>From g_anaeig I can obtain atom fluctuations along defined mode
1- Can I obtain same fluctuations along ensemble of several modes (i.e
averaged fluctuations along modes from n to k ) in one graph ?
2- Is there any w
On 10/11/2011 5:36 PM, James Starlight wrote:
Thank you, Mark.
By the way, also I have some question about data analysing
From g_anaeig I can obtain atom fluctuations along defined mode
1- Can I obtain same fluctuations along ensemble of several modes (i.e
averaged fluctuations along modes
Mark hello,
2011/11/10 Mark Abraham
> From your description, I think you're comparing apples with oranges.
>
>
I just want compare results of coarse grained NMA based on C-alpha only
with full atomic NMA.
I've already done that work and obtain that
1- overal picture of fluctuations is the same
Hi James,
> 1- Can I obtain same fluctuations along ensemble of several modes (i.e
> averaged fluctuations along modes from n to k ) in one graph ?
The total fluctuation is the sum of the fluctuations along all the
modes. To get what you want, you just need to some the fluctuations.
Alternatively
Hi Tsjerk,
Thanks for help. So as I understood if I want to calculate fluctuations
only for Calpha I must first to do NMA of my reference in some mode
subspace consisted of the eigenvectors for Calpha atoms only. Does this
correct ?
Previously I've done something like this for random subspace of m
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