*Dear all,**
*
*I wanted to minimize the energy of a single molecule. How
emtol and emsteps I have to put to get optimised single molecule structure.*
*
*
*Thank you**
*
*
*
*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.
+91-9686933963.*
--
gmx-users
On 4/11/2011 5:14 PM, Ravi Kumar Venkatraman wrote:
*Dear all,**
*
*I wanted to minimize the energy of a single molecule. How
emtol and emsteps I have to put to get optimised single molecule
structure.*
*
Set them to whatever size seems reasonable to you and leaves you with a
Dear all,
I'm trying to FEP away a TIP4P water molecule from a water box in gmx
4.5.3, but getting a jump in dH/dlambda after some time (around 100 ps),
from around -5 to -600 kJ/mol/lambda. I'm using softcore with the
following parameters:
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
Dear sir：
Thank you for reading my letter.
I have a few problems in Shell MD
. I do not know how to set the parameter in the*.mdp file of shell
md.So I hope to obtain your help.
And this is my own *.mdp file below
include =
define =
Dear sir：
Thank you for reading my letter.
I have a few problems in Shell MD
. I do not know how to set the parameter in the*.mdp file of shell
md.So I hope to obtain your help.
And this is my own *.mdp file below
emtol= 10
emstep = 0.01
*Dear All,
Could anybody tell me what is the purpose of Extension of the
potential lookup tables beyond the cut-off. I have read somewhere that the
sum the smallest diagnol of the box and rlist should be equal to
table-extension. Please explain me the same.*
*With Regards,
Ravi Kumar
Dear All
Could any one help me to solve this error in gromacs 4.5.5 version. I am
running dynamics on apo protein and the protein shows negative charge of -6
(after choosing OPLS-AA force filed) and when i was neutralizing the -6
with +6 and generating the genion.tpr file there it shows No such
Dear All
Could any one help me to solve this error in gromacs 4.5.5 version. I am
running dynamics on apo protein and the protein shows negative charge of -6
(after choosing OPLS-AA force filed) and when i was neutralizing the -6
with +6 and generating the genion.tpr file there it shows No such
On 5/11/2011 1:05 AM, kirubakaran palani wrote:
Dear All
Could any one help me to solve this error in gromacs 4.5.5 version. I
am running dynamics on apo protein and the protein shows negative
charge of -6 (after choosing OPLS-AA force filed) and when i was
neutralizing the -6 with +6 and
On 4/11/2011 10:41 PM, Ravi Kumar Venkatraman wrote:
*Dear All,
Could anybody tell me what is the purpose of Extension of
the potential lookup tables beyond the cut-off.*
Check out manual 7.3.12
*I have read somewhere that the sum the smallest diagnol of the box
and rlist
I have seen different articles on MD simulation in vaccum but i didn't get
the exact way for it.If u can tell me the exact way then i can proceed for
it fastly because I have to do it within certain time limit.
On Thu, Nov 3, 2011 at 11:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On
Dear Gromacs users,
I'm attempting to simulate a system composed of two proteins containing a
thioester bond between the C-terminus of chain A and a cysteine residue
from chain B.
I wonder if the parameters for this bond to be included in the .top
file exist. Also, I am having troubles figuring
Thanks for the suggestion.
Also, I was wondering how one can get the time profile of the irreversible
work from the gromacs pull-code out put . From constant pulling-rate SMD, we
get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying
the the value from pullx.xvg and value
Dear Gromacs Users,
I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx
4.5.3). during my initial pull to generate configurations for umbrella windows
I have pulled in the -Z direction,
@ s0 legend 0 Z
@ s1 legend 1 dZ
0. 7.37361 -0.33625
0.0200 7.37377
Anushree Tripathi wrote:
I have seen different articles on MD simulation in vaccum but i didn't
get the exact way for it.If u can tell me the exact way then i can
proceed for it fastly because I have to do it within certain time limit.
It would be useful if you were to describe what it is
alberto arrigoni wrote:
Dear Gromacs users,
I'm attempting to simulate a system composed of two proteins containing
a thioester bond between the C-terminus of chain A and a cysteine
residue from chain B.
I wonder if the parameters for this bond to be included in the .top
file exist. Also, I
*Dear All,
Ok, I don't remember the site. But please explain me about the
purpose of table extension.
Thank you
*
*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.
+91-9686933963.*
--
gmx-users mailing listgmx-users@gromacs.org
nahren manuel wrote:
Dear Gromacs Users,
I am trying to study ligand unbinding adopting Umbrella sampling (using
Gmx 4.5.3). during my initial pull to generate configurations for
umbrella windows I have pulled in the -Z direction,
@ s0 legend 0 Z
@ s1 legend 1 dZ
0.7.37361
Hi Alberto,
I used a stupid method to deal with this kind of non-standard moiety. You
can use AmberTools to parameterize your thioester, together with your
proteins, and then use acpype to convert they topology and coordinate files
to gromacs format. But I am not sure if you want to use amber
Hi Justin,
If you observe my pulling simulation, you will see that the distances are
(increasing) in the negative.
Here is the PMF (image):
http://www.flickr.com/photos/nahrenmascarenhas/6312990056/
this is not one expects in ligand unbinding. (of course these are from my
initial
nahren manuel wrote:
Hi Justin,
If you observe my pulling simulation, you will see that the distances
are (increasing) in the negative.
Exactly as you expect. You're pulling along the -Z dimension, as you said
before. So the ligand is pulled from the protein to an increasingly negative
when i run the given command i.e,
grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
It is showing fatal error:No such molecule type NA.
How could I troubleshoot this problem?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Anushree Tripathi wrote:
when i run the given command i.e,
grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
It is showing fatal error:No such molecule type NA.
How could I troubleshoot this problem?
Ion naming is listed in ions.itp - the NA name works for all force fields
Ravi Kumar Venkatraman wrote:
*Dear All,
Ok, I don't remember the site. But please explain me about
the purpose of table extension.
Please refer to http://manual.gromacs.org/online/mdp_opt.html#table and the
manual, section 6.7.2.
-Justin
--
On 5/11/2011 5:35 AM, Ravi Kumar Venkatraman wrote:
*Dear All,
Ok, I don't remember the site. But please explain me
about the purpose of table extension.
*
Sorry, I have other things to do than refute statements that you can't
attribute, when you don't appear to have managed to
Dear Gromacs Users and Experts,
I want to calculate from my xtc trajectory the B-factor and the
anisotropic temperature factor. I'm using following gromacs command:
$ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb
I want to input the resulting PDB file to the TLS
Hi,
I am performing steered MD simulation using gromacs.
I was wondering how one can get the time profile of the irreversible work from
the gromacs pull-code out put . From constant pulling-rate SMD, we get time
profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the
value
Hi Sanku,
I was using the pullf.xvg and multiplying it with pulling rate and time.
f*v*dt = W
and getting the total work for each SMD simulation.
I'm not sure if this is the best/correct way to do it. But from original
Jarzynski's article (PRL (2007) 78(14), 2690-2693) this is what I deduced.
I
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