Hi all,
I want to perform brownian dynamics simulations using gromacs
4.5.5 for a system containing protein in water. What is the basis to
select the bd_fric value for this system. I came to know through previous
posts that a value of 3000 would be fine for a time step less than 4fs.
Hello, I've got a question. Is there a way to continue MD simulation, not
from last state but from specific time of MD? Say we have made a MD, have
analysed it and have found an interresting molecule conformation at
specific frame. Can we continue from this point or we should extract this
frame,
If the frame was saved to the trajectory file, just extract it with
trjconv -dump $timeframe -o conf.gro
and continue your MD.
No need for any additional energy minimizations, of course.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар gontc...@gmail.com wrote:
Hello,
Aside from original question, you will probably want to initialize
velocities (gen_vel) in order to evolve a different trajectory rather than
repeating previous one.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 1:00 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
If the frame was saved to the
Thanks!
2013/5/29 Dr. Vitaly Chaban vvcha...@gmail.com
If the frame was saved to the trajectory file, just extract it with
trjconv -dump $timeframe -o conf.gro
and continue your MD.
No need for any additional energy minimizations, of course.
Dr. Vitaly Chaban
On Wed, May 29,
If you want to observe H-bond dynamics and do it with an atomistic
precision than, of course, you need an all-atom representation. United
atoms will still *effectively* account for H-bonding, if you are happy with
reduced precision.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 8:01 AM, Revthi
According to my understanding, setting friction coefficient is quite a
personal thing. The higher is bd-fric, the smaller are velocities.
Why not to set bd-fric = 0 in order to start with? See manual for details
of how this trick works.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 11:48 AM,
Dear gmxusers,
I am using gromacs version 4.5.4 and i am simulating a
surface upon base pairs on it. I would like perform simulation with the
GBSA implicit solvent model and I have tried that but one problem occurs
during running. Actually grompp has having some problem with the
Hello, I have a problem.
I try to extending my simulation. I made this steps.
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
I need to put more things on mdrun, or only this? because my first mdrun had 4
or 5 outputs, or the extending recognize de
Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values.
--
regards
M.SathishKumar
--
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Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values.
--
regards
M.SathishKumar
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Hello Sir ,
Thanks for your quick reply. I have used bd_fric =0 and then my
simulation is blowing up. I have used a time step of 0.002ps, Hence i
thought if i can use some other value rather than zero but I do not know
which value to use. Can you suggest any general value for protein
Hello Mohan -
I do not use Brownian dynamics code routinely to have exact values for
various cases, but if I were you, I would start with smaller value and then
increase, until your simulation runs fine. The time-step depends not on the
method, but on characteristic oscillations (bond lengths,
On Wed, May 29, 2013 at 3:14 PM, Fábio Filippi Matioli
fabiof...@hotmail.com wrote:
Hello, I have a problem.
I try to extending my simulation. I made this steps.
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
I need to put more things on
The force should not probably exceed kT product too much...
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 3:19 PM, Sathish Kumar sathishk...@gmail.comwrote:
Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values.
--
Hello,
I am interested in dynamical analysis of my protein. In the manual, it says
-ascii generates a file that includes the whole covariance matrix, and -xpma
writes the atomic covariance matrix per pair of atoms. I was wondering if
there is a way to have this atomic covariaces in the .dat file
I do not remember all the keys.
Rename your files to their default names and you will have nothing to
specify except
mdrun -cpi
On Wed, May 29, 2013 at 6:31 PM, Fábio Filippi Matioli
fabiof...@hotmail.com wrote:
Hello, i'm who asked about extending simulations.
You sad for me pen teh
perhaps mdrun -cpi -deffnm full
will also do the job in your case
On Wed, May 29, 2013 at 6:36 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
I do not remember all the keys.
Rename your files to their default names and you will have nothing to
specify except
mdrun -cpi
On Wed, May
If you want to have the default behaviour of appending new output to the
old files, GROMACS needs to be able to find those files and their content
must be unchanged. If you cannot/will not satisfy that condition, you can
use mdrun -noappend to force GROMACS to simulate on. Making sense of your
On 5/29/13 9:19 AM, Sathish Kumar wrote:
Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values.
There is no systematic way to set these values, at least none that I know of.
Everyone has their own impression of
I'm working on a .GRO file and have come across a formatting error.
In the manual, it states that the spacing for each column in the .GRO file
is:
residue number (5 positions, integer)
residue name (5 characters)
atom name (5 characters)
atom number (5 positions, integer)
position (in nm,
In a system that has no charges, should we observe a difference between
simulations using PME/Cut-offs or Reaction Field?
From my understanding there should not be, since there are no charges which
treatment you use shouldn't' make a difference.
However, it does and I am trying to work out
Dear Gromacs users!
In some discussions I've noticed that people told about usage of virtual
sites which allow to increase time step of the simulation of such systems.
From manual and tutorial its not quite understand for me how with inclusion
of such dummy atoms (which can be used to reduce
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