Hello, gmx-users,
I have some problems with the "gmxdump" order. How to transform the traj.trr
to
another readable file every two steps? In another word, there are 1 frames
in
the traj.trr file. I would like to transform datas every second frame in the
traj.trr to another readable file. H
Hi Peggy,
This is very much basic stuff for which you should refer to the
manual/wiki. E.g. on the index file, look at
http://wiki.gromacs.org/index.php/Index_File
For the other questions, check the manpages of editconf, trjconv and tpbconv.
Cheers,
Tsjerk
On Thu, Apr 10, 2008 at 11:03 PM, Pe
曹臻 wrote:
Hello, gmx-users,
I have some problems with the "gmxdump" order. How to transform the traj.trr
to
another readable file every two steps? In another word, there are 1 frames
in
the traj.trr file. I would like to transform datas every second frame in the
traj.trr to another reada
Andreas Kring wrote:
Hello all,
I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules,
density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This
works out fine, i.e. I get a correct radial distribution function
(g_OO), but the heat capacity (C_V) is wrong. I ca
Hello all,
I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules,
density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This
works out fine, i.e. I get a correct radial distribution function
(g_OO), but the heat capacity (C_V) is wrong. I calculated it using the
Dear all,
I had been running many runs of mdrun in a Sun opteron
cluster with each node having 4 processors.
When I ran my latest mdrun after 15ns run, I get the
following error and mdrun exits without any error
message on other log files.
***
mp
Dear list,
The OPLS parameter for S in DMSO is zigma 0.395 and epsilon 3.56 A
( JACS 1996, 118, 4175-4180)
But in the ffoplsaanb.itp (/gromacs/3.3.2-dp/share/gromacs/top) it is given as
below:
-
name bond_typemass
Ragothaman Yennamalli wrote:
Dear all,
I had been running many runs of mdrun in a Sun opteron
cluster with each node having 4 processors.
When I ran my latest mdrun after 15ns run, I get the
following error and mdrun exits without any error
message on other log files.
***
Hi all
How can I count the number of water molecules within spheres of desired
radii around a solute when I analyse the trajectory.Thank you in advance!
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[EMAIL PROTECTED] skrev:
Hi all
How can I count the number of water molecules within spheres of desired
radii around a solute when I analyse the trajectory.Thank you in advance!
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JMandumpal wrote:
Dear list,
The OPLS parameter for S in DMSO is zigma 0.395 and epsilon 3.56 A
( JACS 1996, 118, 4175-4180)
But in the ffoplsaanb.itp (/gromacs/3.3.2-dp/share/gromacs/top) it is
given as below:
-
namebo
I'm doing a dynamic of a peptide in a mixture TFE/H2O ( 30/70 %).
I'm using this file.mdp :
cpp = /lib/cpp
define = -DFLEX_SPC -DPOSRES
constraints = all-bonds
integrator = md
tinit = 0.0
dt = 0.002 ; ps !
nsteps = 50 ; total 1000 ps.
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 0
nst
Thank you, Tsjerk. I will check them out.
But I am still confursed with what has gone wrong. As I said in my previous
eamil, in fact, 2 Ca atoms are a part of the protein. They are in the PDB
file passed to pdb2gmx. Water molecules are added after the protein atoms
and the Ca atoms, as in the PDB
Hi everyone.
I'm interested in running a steered MD simulation of a protein +
inhibitor complex with the aim of reproduce the large conformational
changes that are experimentally demonstrated to occur during ligand
binding. Can I be able to reproduce such big conformational changes
through SMD sim
Dear gmx-users,
Greetings.
I try to have methane pdb. or CO2.pdb to understand basically how to
have a vibrational mode.
But I have problem with imput pbd file.
ATOM 1 C1METH1 3.875 0.678 -8.417 1.00 0.00
ATOM 2 H1 METH1 3.800 1.690 -8.076 1.00 0.
Hello,
Your atoms coordinates are too far away from each other.
Try to paste the text below into a new text file. Make sure to rename it
to a .pdb extension. Voila!
Cheers.
Ps. This is a Methan molecule.
HEADER METHANE
HETATM1 C 1 0.257 -0.
Dear all.
Please, How can I do to have MTH this force field.
MTH ffgmx.rtp - methanolCH3OH
Thanks a lot
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Please search the arch
I need help on how to uninstall gromacs so that i can recompile it again to
enable MPI support, so that i can run gromacs in parallel.
But first i need to know if that is possible and even if it has any
advantage since i am running gromacs on a intel core 2 quad processor, which
supposedly has 4 pr
fabracht sdf wrote:
I need help on how to uninstall gromacs so that i can recompile it again
to enable MPI support, so that i can run gromacs in parallel.
You don't need to uninstall, you just need to follow the instructions on
the GROMACS webpage.
But first i need to know if that is possibl
Peggy Yao wrote:
Thank you, Tsjerk. I will check them out.
But I am still confursed with what has gone wrong. As I said in my
previous eamil, in fact, 2 Ca atoms are a part of the protein. They are
in the PDB file passed to pdb2gmx. Water molecules are added after the
protein atoms and the Ca
Collins Nganou wrote:
Dear all.
Please, How can I do to have MTH this force field.
MTH ffgmx.rtp - methanolCH3OH
Firstly, you haven't described what you are trying to do. Secondly,
ffgmx is deprecated, and should not be used for new simulations.
Mark
___
Thank you for your reply, integrate the rdf can only provide the average
hydration
number, but I want to calcualte the dependence of hydration on the time, namely
the number of water molecules within the some radii around the solute.
In your mail:
>From: David van der Spoel <[EMAIL PROTECTED]>
You can actually do what you want in VMD.
Cheers,
Michel
On Fri, Apr 11, 2008 at 10:38 PM, <[EMAIL PROTECTED]> wrote:
> Thank you for your reply, integrate the rdf can only provide the average
> hydration
> number, but I want to calcualte the dependence of hydration on the time,
> namely
> th
[EMAIL PROTECTED] wrote:
Thank you for your reply, integrate the rdf can only provide the average
hydration
number, but I want to calcualte the dependence of hydration on the time, namely
the number of water molecules within the some radii around the solute.
So partition your trajectory with
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