Dear All,
We have started our venture into MD recently, for which we are using our
in-house resources. Now that MD runs are giving very large output files
like for trr files. The files keep piling up and using spaces on the
work machines. This is creating problems with the depletion of space
w
That sounds more reasonable...:)
In fact I like the idea of using distance restraints, but I still doubt,
that will work...
I would really suggest to use the TI method. If you apply it properly it
should give reasonable results. With proper application, speaking about
using soft-core for VdW
Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goetti
Thank u very much for your suggestion, and now I had get the .gro file and .top file of ATP molecule, but how to I add the ATP molecule into the .gro and .top files of the protein? (If I paste the ATP's datas to the end of protein's file directly, and do genbox, then the result (.gro /.top file) on
Hi,
As long as you have the exact date you checked it out from CVS it is
possible to obtain the same version again.
However, bear in mind that CVS _does_ break periodically, and we
don't check it like the released version. Before I do anything
production-related with CVS I always check th
Dear Mark,
Thanks for the reply.
I am using the following options for the electrostatics in the mdp file
coulombtype = pme
fourierspacing = 0.1
pmeorder= 4
optimize_fft= yes
ewald_rtol = 1.0e-5
ewald_geometry = 3dc
So if I understood you correc
As Mark suggested. If you have the parameters for your ATP, build an
RTP-entry and afterwards, give the protein together with ATP into pdb2gmx...
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettinge
Yes, I found a server (ProDrg) can get the .gro and .top files of ATP
molecule.
---
Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.
Maik Goette, Dipl. Biol.
Max Planck Ins
Mark Abraham wrote:
> Gurpreet Singh wrote:
>> I get the following errors while using paralled version of mdrun compiled
>> with openmpi.
>> mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1
>> *
>> Program mdrun_d_mpi, VERSION 3.3.99_development_20070720
>> Source code file: gmx_parallel_3dfft.c
singh wrote:
Dear Mark,
Thanks for the reply.
I am using the following options for the electrostatics in the mdp file
coulombtype = pme
fourierspacing = 0.1
pmeorder= 4
optimize_fft= yes
ewald_rtol = 1.0e-5
ewald_geometry = 3dc
So if I under
Be aware, that you can't use the ouput with every forcefield...
Attaching the gro-file to your protein gro at the proper position (right
after the protein) and building the correct topology should do the job.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical &
Monika Sharma wrote:
Dear All,
We have started our venture into MD recently, for which we are using our
in-house resources. Now that MD runs are giving very large output files
like for trr files. The files keep piling up and using spaces on the
work machines. This is creating problems with the
Hi Monika,
use
trjconv -f your_trr_file_is_big.trr -o your_trr_file_is_compresses.xtc
after your run.
or change the frequencies for writing out coordinates, velocities etc in your
mdp file like:
nstvout = 1000; frequency to write velocities to output trajectory,
Thanks Mark for your reply. Thats a sound advice. I will really take
care of. Actually, through my previous mail, I wanted to know that what
other groups are using as storage devices for the backup of their large
files, that must have figured out that which way is best-" economical
and efficien
I've always used HDDs for the main backup/working copies, and DVDs for
longer-term backup. You can get hold of 100x spindles of DVDs quite cheaply
these days... I wouldn't call it convenient, though.
- Original Message
From: Monika Sharma <[EMAIL PROTECTED]>
To: Discussion list for GR
This is an interesting topic and has been discussed before:
http://www.gromacs.org/component/option,com_wrapper/Itemid,165/
We use a tape-drive for backups.
/Erik
9 aug 2007 kl. 11.56 skrev Alan Dodd:
I've always used HDDs for the main backup/working copies, and DVDs
for longer-term backup.
Dear Mark,
As you suggested, i ran the simulations with fourier spacing of
0.08,0.09,0.10 & 0.11 with mpirun -np 4 mdrun_d_mpi -np 4
following is the output
fourierspacing =0.08
---
Program mdrun_d_mpi, VERSION 3.3.99_development_20070720
Sourc
Hi,
If you are using any of the united atom GROMOS96 forcefields then there is
already an rtp entry for ATP. Check out the .rtp files in the top folder.
All you need to do is to have the ATP atoms in the pdb file the same as the
atom names in the .rtp file for pdb2gmx to do all the work for yo
The system is a protein binding with one ligand and the ligand mutates to
another one. The problem is found when lamda=1. First of all I run a energy
minimization using an initial structure from the product of lamda=0.9. Then
the problem happens when I run a equilibrium.
Here is the mdp option:
cpp
Dear all,
I have encountered noticeable differences while using the pull code with
the -shuffle -sort options in parallel, as opposed to running in serial
or in parallel without the options. Using -shuffle -sort, the dynamics
of the molecule of interest appears to be unaffected by the pulling
Sorry 'bout that, this time with the files...
Gromacs Runs One Microsecond At Cannonball Speeds
2
1ETHET11 0.769 0.769 0.744
1ETHET22 0.769 0.769 0.794
1.53748 1.53748 1.53748
#include "ffgmx.itp"
#include "OneEthane.itp"
[ system ]
;Name
pure etha
Hi, I'm doing a comparison in the aspect of speed between gromacs and an
other MD-simulation-program, that isn't providing all the diffrent
options of gromacs.
My problem is, that the results I got from the simulations with gromacs
aren't reasonable. E.g negative pressure and zero kelvin or ri
Hi,
> I have been reading your work about free energy calculations and it is
> impressive. I want to estimate binding free energy for a ligand/receptor
> complex and I would appreciate your valuable input on how to approach the
> system I am using. It is the first time I attempt free energy
> cal
Carsten Kutzner wrote:
Mark Abraham wrote:
Gurpreet Singh wrote:
I get the following errors while using paralled version of mdrun compiled
with openmpi.
mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1
*
Program mdrun_d_mpi, VERSION 3.3.99_development_20070720
Source code file: gmx_parallel_
Nicolas Schmidt wrote:
Hi, I'm doing a comparison in the aspect of speed between gromacs and an
other MD-simulation-program, that isn't providing all the diffrent
options of gromacs.
My problem is, that the results I got from the simulations with gromacs
aren't reasonable. E.g negative pressu
>
> Maybe it should be obvious, but (a) why are you constraining two
> distances, and (b) are you sure your constraints aren't going to muck
> with the internal degrees of freedom for the ligand? I would think one
> would like to pull the ligand out of the receptor along some
> particular directio
I have encountered noticeable differences while using the pull code with
the -shuffle -sort options in parallel, as opposed to running in serial
or in parallel without the options. Using -shuffle -sort, the dynamics
of the molecule of interest appears to be unaffected by the pulling
potential.
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