when i ran gromacs to produce topology file for a nucleotide sequence it is
showing the above error saying There is a dangling bond at at least one of
the terminal ends and the force field does not provide terminal entries or
files. Edit a .n.tdb and/or .c.tdb file. i tried giving the starting
Dear All,
The value of the energy of the hydrogen bond has relation with distance and
angle of the hydrogen bond related atoms. As for in the simulation process, the
distance and angle of the hydrogen bond related atoms may change continuously.
Will you please let me know based on which
On 31/05/2012 4:42 PM, Acoot Brett wrote:
Dear All,
The value of the energy of the hydrogen bond has relation with
distance and angle of the hydrogen bond related atoms. As for in the
simulation process, the distance and angle of the hydrogen bond
related atoms may change continuously. Will
On 31/05/2012 4:13 PM, ramaraju801 wrote:
when i ran gromacs to produce topology file for a nucleotide sequence it is
showing the above error saying There is a dangling bond at at least one of
the terminal ends and the force field does not provide terminal entries or
files. Edit a .n.tdb
On 31/05/2012 11:24 AM, Andrew DeYoung wrote:
Hi,
I have a system in a slab geometry. A surface exists at z = 0; many
hydrogens protrude from the surface, and these hydrogens are mostly (but not
precisely) immobile. Above the surface, there is liquid, including the
anion BF4- (tetrahedral
Hi Mark,
It is confusing. As you know, for the same hydrogen bond in a protein, the
related hydrogen bond angle and bond length can vary within a scope during the
whole simulation process, however this small vibration of the hydrogen bond
angle and length can lead to significant energy change,
On 31/05/2012 7:46 PM, Acoot Brett wrote:
Hi Mark,
It is confusing. As you know, for the same hydrogen bond in a protein,
the related hydrogen bond angle and bond length can vary within a
scope during the whole simulation process, however this small
vibration of the hydrogen bond angle and
--- On Wed, 30/5/12, patrick wintrode pat_w...@yahoo.com wrote:
After creating a box using editconf and then solvating using genbox, I try
to add ions and get the infamous number of coordinates in .gro does not
match number of coordinates in topology error.
I've had this problem after
Hi all,
There must be something I don't fully understand, by running grompp on a
system, I get this:
Estimate for the relative computational load of the PME mesh part: 0.32
Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which is the recommended
value for a dodecahedral box. But then
According to the manual, mdrun does not dedicate PME nodes unless -np 11
You can manually specify dedicated PME nodes using -npme, but it is highly
system dependent on whether this will be faster on lowcore systems.
Also the estimate given by grompp may not be optimal during runtime. You'll
have
On 31/05/2012 9:11 PM, Ignacio Fernández Galván wrote:
Hi all,
There must be something I don't fully understand, by running grompp on a
system, I get this:
Estimate for the relative computational load of the PME mesh part: 0.32
Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which
how to assign charge and charge group number when new residue as being
added to the existing amino acid rtp file
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On 31/05/2012 9:37 PM, Subramaniam Boopathi wrote:
how to assign charge and charge group number when new residue as being
added to the existing amino acid rtp file
Read about the file format in the manual.
Mark
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On 5/31/12 7:37 AM, Subramaniam Boopathi wrote:
how to assign charge and charge group number when new residue as being added to
the existing amino acid rtp file
The details depend on the force field you're using.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
--
Dear justin
Thank you for your previous reply
Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5) first of
all i have successfully installed debain package of gromacs-openmpi
for that i have configured and compiled using the following command
./configure
On 31/05/2012 10:17 PM, vidhya sankar wrote:
Dear justin
Thank you for your previous reply
Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5)
first of all i have successfully installed debain package of
gromacs-openmpi
for that i have configured and compiled
Dear All,
I have no clue what specifically you are trying, but I feal bad for all the
physicist and quantum chemist whom have provided the software and continued to
develop it.
Scanning in my free time, it seems a large amount of confusion on what people
are trying to do stems from
Michael,
Thank you for your answer. On the other hand, I´m not implementing, I´m
using REMD.. I miss wrote it.
Nathalia
-Mensaje original-
De: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] En
nombre de Michael Shirts
Enviado el: lunes, 28 de mayo de 2012 08:09
On 5/31/12 8:17 AM, vidhya sankar wrote:
Dear justin
Thank you for your previous reply
Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5) first of
all i have successfully installed debain package of gromacs-openmpi
for that i have configured and compiled using the following
Hi All,
I really need to know how to apply long range LJ correction to calculate
surface tension of TIP4P/2005 water. I can get 65 dyn even i use vdw cut-off =
1.4 nm, but from the reference people can get 69 dyn.
I included the LJ Long range LJ correction using the following .mdp,
please note
On 1/06/2012 12:18 AM, MD wrote:
Hi All,
I really need to know how to apply long range LJ correction to
calculate surface tension of TIP4P/2005 water. I can get 65 dyn even i
use vdw cut-off = 1.4 nm, but from the reference people can get 69 dyn.
I included the LJ Long range LJ correction
Mark,
Thank you SO much for your help. I will try these suggestions. You're
awesome.
Andrew
Hi,
I have a system in a slab geometry. A surface exists at z = 0; many
hydrogens protrude from the surface, and these hydrogens are mostly (but
not
precisely) immobile. Above the surface, there
Hi,
Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy
between two groups (say NH---CO) by using the Kabsch and Sander function
described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637).
Quoting: E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 =
Dear justin ,
Very very thanks for your previous patience reply
When i run the mpi calculation using more than one node (each node have 16
processor) which option do i need to use in the following command may i use
-npme option?
mpirun -np 19 mdrun_mpi_d -s toplo.tpr
Thanks
On 5/31/12 12:00 PM, vidhya sankar wrote:
Dear justin ,
Very very thanks for your previous patience reply
When i run the mpi calculation using more than one node (each node have 16
processor) which option do i need to use in the following command may i use
-npme option?
mpirun -np 19
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Hi,
I am trying to calculate a PMF for an ion along a channel. Everything went OK,
but when I used g_wham I got a profile with strange dimensions for the x-axis.
What are the boundaries g_wham is using for calculating the units of x-axis?
I have used:
g_wham -it tpr-files.dat -if
On 5/31/12 1:20 PM, Rebeca García Fandiño wrote:
Hi,
I am trying to calculate a PMF for an ion along a channel. Everything went OK,
but when I used g_wham I got a profile with strange dimensions for the x-axis.
What are the boundaries g_wham is using for calculating the units of x-axis?
The
Thanks a lot for your quick answer.
The mdp file I have used is copied below. What is strange is that when I look
at the *gro files for the different windows (100 windows in total), i. e:
window 1: 8704Na Na56458 5.134 5.085 5.824
window 50: 8704Na Na56458 5.053 5.081
Dear all,
does anyone know of any MD or gromacs training course in the coming months?
All the best
g-
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On 5/31/12 1:38 PM, Rebeca García Fandiño wrote:
Thanks a lot for your quick answer.
The mdp file I have used is copied below. What is strange is that when I look at
the *gro files for the different windows (100 windows in total), i. e:
window 1: 8704Na Na56458 5.134 5.085 5.824
window 50:
Hi List,
Has anybody have something else to add to the Peter's comments?
Basically, I'm still unsure about modeling deletions.
Any help is appreciated.
Em 30-05-2012 17:37, Peter C. Lai escreveu:
You might be able to use MODELLER for generating the helix deletions since
it is alignment-based.
Thanks again, and sorry for insisting, but I am not sure of understanding it
totally.
So, the boundaries g_wham calculates are not related to the dimensions of my
channel? Would be any way to convert these units into the position of the ion
in the channel in each case?
Thanks again a lot for
On 5/31/12 1:58 PM, Rebeca García Fandiño wrote:
Thanks again, and sorry for insisting, but I am not sure of understanding it
totally.
So, the boundaries g_wham calculates are not related to the dimensions of my
channel? Would be any way to convert these units into the position of the ion in
Where is the center of mass of reference group (MOL) located?
It seems that the COM is near the middle of the ion channel. Since you
use 'pull_geometry=distance', g_wham will look only for the distance
between 'MOL' and 'Na' and that leads to problem.
If the com of 'MOL' sits in the center of
Hi,
the center of mass of my channel is at the middle of the ion channel, and it is
a symmetric system, so I suppose these results would be OK. Anyway, I will
check the options you propose.
Thanks a lot for all your comments!!
Best wishes,
Rebeca.
Date: Thu, 31 May 2012 20:08:26 +0200
From:
On 5/31/12 3:37 PM, Rebeca García Fandiño wrote:
Hi,
the center of mass of my channel is at the middle of the ion channel, and it is
a symmetric system, so I suppose these results would be OK. Anyway, I will check
the options you propose.
If you are sampling regions above and below the
On 5/31/12 3:51 PM, Rebeca García Fandiño wrote:
OK,
however, just one point about your last comment:
I suspect this is why g_wham is finding a range of values only equal to half
of
your expected reaction coordinate; it is considering only the positive
displacement along the reaction
Yes,
my profile seems normal, the only problem are the units in the x-axis, because
I expected them to be in the range of the dimensions of the channel.
I will try if I see differences with the other options you proposed, anyway.
Thanks a lot for your help!!
Best wishes,
Rebeca.
Date: Thu, 31
OK,
however, just one point about your last comment:
I suspect this is why g_wham is finding a range of values only equal to half
of
your expected reaction coordinate; it is considering only the positive
displacement along the reaction coordinate.
It seems like all the channel is
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