Hi!
I want to calculate energy from GROMOS96-GB/SA. What command should
be used?
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Hi,
if you are interested in a particular angle (between a triad of atoms) you
can specify it in angle.ndx file (to generate the angles run: mk_angndx -s
topol.tpr -n angle.ndx)
the -ov flag of g_angle will generate the angle trajectory and the -od flag
will generate its distribution
cheers
On
simon sangma wrote:
Hi!
I want to calculate energy from GROMOS96-GB/SA. What command
should be used?
g_energy
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Maurício Menegatti Rigo wrote:
IS this a problem?
/System has non-zero total charge: -8.01e+00/
If yes, can I fix that changing COulomb cutt-off to PME electrostatics?
You need to add counterions to your system. Consult some basic tutorial
material, as well as the manual entry for
Dear all:
These days, I am trying to pull a slab of griphene moving along the Z direction
at a constant speed. The slab of griphene contains 700 atoms. After several
times of E-mail communication with the Gromacs users, the simulation can run.
However, the run didn't produce the results which
You should always neutralise your sysem.
On Thu, Feb 25, 2010 at 1:42 PM, Maurício Menegatti Rigo
mauriciomr1...@gmail.com wrote:
IS this a problem?
*System has non-zero total charge: -8.01e+00*
If yes, can I fix that changing COulomb cutt-off to PME electrostatics?
THanks!!
--
Hi ,
I have a protein with 2 chains. I need to do normal mode analysis on it.
As there are no
covalent bonds between the two chains, I did not use the merge option in the
pdb2gmx
command.
I am trying to energy minimize the structure , in vaccum.( in double precision)
, but am not
able
Dear gmx users,
I am sorry to ask this question again, but reading in the email achieve did not
enlighten me. I found this email which describes my problem, but unfortunately
it has no replies:
http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html
Also there are these two
Sarah Witzke wrote:
Dear gmx users,
I am sorry to ask this question again, but reading in the email achieve did not
enlighten me. I found this email which describes my problem, but unfortunately
it has no replies:
http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html
Thank you for your quick respons! It is not so much the drop, but more the
position and the prescens of a small drop, then a little rise and then the big
drop. I have pasted the file in below.
Do you think my method of replacing the order parameters for the double bonded
atoms is ok?
Thank you for your replies,
indeed it worked!
But now, I'm looking for a command line that allows me to calclulate the
RMSF (or if you prefer, the distance between Calpha) between 2 static
structures.
Carla
On Thu, Feb 25, 2010 at 11:55 AM, Amir Marcovitz amarcov...@gmail.comwrote:
Hi,
if
On 26/02/2010 1:11 AM, Carla Jamous wrote:
Thank you for your replies,
indeed it worked!
But now, I'm looking for a command line that allows me to calclulate the
RMSF (or if you prefer, the distance between Calpha) between 2 static
structures.
Look in section 7.4 of the manual for a run-down
Sarah Witzke wrote:
Thank you for looking at the data. I just thought, that it deviated too much
from published results, but perhaps it is because I have mainly worked with
saturated lipids. I calculated the order over the last 117 ns of a 167 ns
trajectory (10 ps between each frames), so
Dear all,
I am sorry for poorly describing my problem about the freezing group size.
Here I am giving my question very briefly, can anybody help me please?
I would like to know the relation between the size of freezing group and the
temperature coupling. when I separate the temperature coupling
Actual text input / output would be a good idea here. What is the actual
output when you try to run it the second time?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
Dear Sir,
I am facing one problem regarding generation of Free energy
landscape (FEL); I have some doubt regarding the algorithm of g_sham. I will be
highly obliged if you kindly let me clear my doubt. I know that three variables
are needed for construction of 3D energy landscape.
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