hello
In gromacs4.0, i want to do a constant force pulling,how to write the
ppa file.
thinks very much.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear Professor Spoel.
I have a question concerning your article on the SW water model
published in J. Phys. Chem. B, 105, 2618-2626 (2001). I guess the
question is only indirectly related to GROMACS, but I'll post in on the
mailing list since it may be of interest to other GROMACS users as
Hello gmx-users,
my aim is to simulate a big nafion polymer in water system.
I already succeded in simulating one nafion monomer in water by following
the classical method (writing a .pdb file, defining residues in .rtp,
defining .itp and so on).
Now i'm facing two new difficulties.
First i
Hi All,
I am analyzing the h-bond information for a mdrun using g_hbond. Can I know
the % of trajectory time for which a bond between particular residue was
existing?
If anybody have tried such option please suggest me a way to do so.
With thanks,
Vivek
Dear all,
I want to simulate an aqueous solution containing sodium and chloride
ions
using a shell model in which I have both LJ and Buckingham
potentials. I am trying
to move away from Åqvist ions and standard water models because
I will be interfacing this solution to a solid and want
Dear all,
I used g_hbond to count the number of hydrogen bonds
between two molecules. The result was here:
# g_hbond_mpi is part of G R O M A C S:
#
# GROningen MAchine for Chemical Simulation
#
@title Hydrogen Bonds
@xaxis label Time
@yaxis label Number
@TYPE xy
@ view 0.15,
Andreas Kring wrote:
Dear Professor Spoel.
I have a question concerning your article on the SW water model
published in J. Phys. Chem. B, 105, 2618-2626 (2001). I guess the
question is only indirectly related to GROMACS, but I'll post in on the
mailing list since it may be of interest to
vivek sharma wrote:
Hi All,
I am analyzing the h-bond information for a mdrun using g_hbond. Can I
know the % of trajectory time for which a bond between particular
residue was existing?
If anybody have tried such option please suggest me a way to do so.
Have you started with reading
Gabriel Marchand wrote:
Hello gmx-users,
my aim is to simulate a big nafion polymer in water system.
I already succeded in simulating one nafion monomer in water by following
the classical method (writing a .pdb file, defining residues in .rtp,
defining .itp and so on).
Now i'm facing two new
Hello,
I tried from the beginning to test gromacs-4.0.2 with a monoclinic system on 8
processors (one two quad core machine). The skew errors seem to be gone, yet
other errors appeared.
Now after a successful md, taking the output and trying to do annealing I get
the following error:
Fatal
HI Mark,
thanks for your reply.
I have gone through the g_hbond -h, and have plotted hbnum.xvg using -num,
which gives me the plot of the number of h_bonds with respect to time,
but can I find out the duration of bond in percent of the whole
trajectory time ?
Please help me if there is
Hello,
So this command used to work fine:
editconf -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0
Now, with gmx 4.0 (from fink for Mac Intel Leopard), I got a warning:
WARNING: No boxtype specified - distance condition applied in each
dimension.
(no box information is inserted in the pdb
vivek sharma wrote:
HI Mark,
thanks for your reply.
I have gone through the g_hbond -h, and have plotted hbnum.xvg using
-num, which gives me the plot of the number of h_bonds with respect to
time, but can I find out the duration of bond in percent of the
whole trajectory time ?
hello friends
for doing normal mode analysis i am trying to create .mtx file .but in
output i am not getting thi .mtx file..what all precautions i have to take
with thanks
On 11/20/08, vivek sharma [EMAIL PROTECTED] wrote:
Hi All,
I am analyzing the h-bond information for a mdrun using
Hey Alan,
I think there is a litle bug in editconf. If you add a CRYST1 line with
some random numbers into the first Complex.pdb, editconf works fine adds
the corret CRYST1 line according to your option (-d and -bt).
Best, Jochen
Alan wrote:
Hello,
So this command used to work fine:
minnu vijayan wrote:
hello friends
for doing normal mode analysis i am trying to create .mtx file .but in
output i am not getting thi .mtx file..what all precautions i have to take
with thanks
To get the attention of someone who deals with normal modes, it would be best to
start a new
Hello,
recently after adding spc water to a structure I have notice that the
molecules have been added to internal cavities. Even though this
situation is possible, for example water could get inside during
folding, this could cause artificial movement of aminoacids being
pushed from inside by
Hi,
I assume this is 4.0 and not 4.0.2, right?
I fixed the problem of not having a box in editconf in 4.0.2.
Berk
Date: Thu, 20 Nov 2008 16:22:44 +
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] problems with editconf 4.0
Hello,
So this command used to work fine:
Hello all,
Recently, I got weird results from my simulations. My NVT system
contains about 300 molecules, which are looks similar to the C60
fullerenes but a little bit modified.
I simulated them with two conditions:
1) constrained bonds
2) harmonic bonds
The problem is this:
When I
Hi,
Do you have anisotropic pressure coupling turned on?
Could you send me the tpr file?
Berk
Date: Thu, 20 Nov 2008 14:47:53 +
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] parallelization error? gromacs-4.0.2
Hello,
I tried from the beginning to test
Thomas Schlesier wrote:
Hi all,
Sorry that this question is not purely related to GRMOACS. Does anybody
know an free program with which it is possible to save a trajektorie as
a movie? With ngmx and VMD i can visualize the trajektorie but i can not
save it as a movie (with VMD only snapshots
Hi,
Ah, so you have anistropic pressure coupling on.
I forgot to put in a check for that when chosing the domain
decomposition grid.
Changing line 200 of src/mdlib/domdec_setup.c from:
if (box[j][i] != 0)
to
if (box[j][i] != 0 || ir-deform[j][i] != 0 ||
Dear all,
To understand the exact parameters used in oplsaa force field, I read
the ffoplsaa*.*** files.
But I can not find all the corresponding atom types in the ffoplsaa.rtp
and ffoplsaabon.itp files.
for example, in rtp file, there is a bond between atom type CG and OG1.
But in
friendli wrote:
Dear all,
To understand the exact parameters used in oplsaa force field, I read
the ffoplsaa*.*** files.
But I can not find all the corresponding atom types in the ffoplsaa.rtp
and ffoplsaabon.itp files.
for example, in rtp file, there is a bond between atom type CG and
Thank you Justin.
Can you tell me how i can find the link between atom names and atom types?
The thing I wanna do is to figure out the bond parameters(b0,bk), and so
the angle, dihedral parameters in oplsaa FF.
Is it possible to give me some examples, such as the bond between CG and
OG1 in
friendli wrote:
Thank you Justin.
Can you tell me how i can find the link between atom names and atom types?
That is listed in the .rtp:
; name typechargecgnr
CGopls_2350.500 3
The thing I wanna do is to figure out the bond parameters(b0,bk), and so
the angle,
In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type
opls_235 and opls_236.
While in oplsaanb.itp, the atom type opls_235 and opls_236 corresponds
to atom name(as display in titles in oplsaanb.itp) C and O.
why there are two different names for the same atom? what is the
friendli wrote:
In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type
opls_235 and opls_236.
While in oplsaanb.itp, the atom type opls_235 and opls_236 corresponds
to atom name(as display in titles in oplsaanb.itp) C and O.
why there are two different names for the same atom?
So to obtain the parameters(e.g. bonds) in topology file,
1, read bond atoms in .top (e.g. 1 2)
2, find atom types of the bond atoms in .top (e.g. oplsaa_235,
oplsaa_236)
3, find atom names of the above atom types in ffoplsaanb.itp (e.g. C, O)
4, check parameters in ffoplsaabon.itp
I look at the .top file generated by grompp (-pp).
However, for me it is more like a copy of all the force field files
into one .top file, so the content are the same as individual ones.
Do I miss anything?
Thank you
Qiang
Justin A. Lemkul wrote:
friendli wrote:
Thank you Justin.
Can
friendli wrote:
So to obtain the parameters(e.g. bonds) in topology file,
1, read bond atoms in .top (e.g. 1 2)
2, find atom types of the bond atoms in .top (e.g. oplsaa_235,
oplsaa_236)
3, find atom names of the above atom types in ffoplsaanb.itp (e.g. C, O)
4, check parameters in
friendli wrote:
I look at the .top file generated by grompp (-pp).
However, for me it is more like a copy of all the force field files
into one .top file, so the content are the same as individual ones.
Do I miss anything?
No, that's how it works. See
friendli wrote:
Hi Mark,
the atom types in .top file is opls_???, but the atom types(or name)
in [bondtypes] in ffoplsaabon.itp file is C, H, CT, C_3, etc.
So we still need to look up ffoplsaanb.itp to link these two atom type
(or name), right?
OK, whatever... as I said, different force
33 matches
Mail list logo
