Dear gurus,
I'm trying to calculate some statistics for the coulomb-sr and
coulomb-recip energies in my system (200 ns simulation). I Suppose the
underlying algorithms in g_energy and g_analyze for making the error
estimate are pretty much the same, but in g_energy the sampling is
more accurate
Dear friends
Unfortunately my MD run got stopped. While i tried to append
the run with command line
mdrun -s fws_md.tpr -cp state.cpt -append, its not get
appending, its again get restart.
What should be the problem.I need to append my run.
--
On 10/3/12 12:06 AM, naga sundar wrote:
Dear Pramod
use the command
xmgrace -nxy file1.xvg file2.xvg
Instead of file1 and file2 use ur file name.
Distance plots produced by g_dist have four data sets (distance and x,y,z
components)
On 10/3/12 12:22 AM, rama david wrote:
Thank you Justin for your reply ,
I tried g_density again after your reply. But I found that
it give density with respect to box dimension and not to time.
I suggested before that you could perhaps advantageously using the -b and -e
flags to achieve
On 10/3/12 6:10 AM, naga sundar wrote:
Dear friends
Unfortunately my MD run got stopped. While i tried to append
the run with command line
mdrun -s fws_md.tpr -cp state.cpt -append, its not get
appending, its again get restart.
-cp is not a valid option.
On 10/3/12 6:00 AM, tarak karmakar wrote:
Dear All,
Is it possible to deal a protein with tyrosyl radical in Molecular
Dynamics Simulation ?? If possible can you please provide me the
reference or literature where I can find the force field parameters
for tyrosyl radical ?
Molecular
On 10/3/12 1:59 AM, James Starlight wrote:
Justin,
I've told about lower lipid density at the left and right edges of the
new system ( see new pic bellow with marked regions).
http://imageshack.us/photo/my-images/10/dppc.png/
I've started with system consisted of 118 lipids and 6000 water
On 10/3/12 1:40 AM, Ashok Kumar Das wrote:
Dear Dr. Justin A. Lemkul,
I am Dr. Ashok Kumar Das from IHPC, Singapore.
I am a new GROMACS learner.
The system I wish to simulate contains 125 polymer
chains, each chain containing 8 beads (CH3 and CH2 groups).
These beads do not have any charge
Thanks justin got it...
On Wed, Oct 3, 2012 at 4:10 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/3/12 6:10 AM, naga sundar wrote:
Dear friends
Unfortunately my MD run got stopped. While i tried to
append
the run with command line
mdrun -s fws_md.tpr -cp
Thanks Justin,
Actually if I would remove the proton from the tyrosine -OH and add
the corresponding charge of the Hydrogen to the phenolic oxygen to
keep the residue neutral then wouldn't it be convenient to think as if
it's a radical ?
On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul
On 10/3/12 7:49 AM, tarak karmakar wrote:
Thanks Justin,
Actually if I would remove the proton from the tyrosine -OH and add
the corresponding charge of the Hydrogen to the phenolic oxygen to
keep the residue neutral then wouldn't it be convenient to think as if
it's a radical ?
That
It's a radical approach, for certain! But do mind that the tyrosyl
side chain is a conjugated system, so the charge goes all over the
place, and you have to do (proper) QM calculations to see where it
ends up. Radical approaches are not suitable for radical parameters :p
Tsjerk
On Wed, Oct 3,
Justin,
Might the modifications of the vdwradii.dat be suitable for such
system expanding or (on other hand) reduction (as in the below picture
are shown). In the lattter case I defined new box dimensions (smaller
than initial box dims) and would like to remove all side water-lipids
layer which
On 10/3/12 8:59 AM, James Starlight wrote:
Justin,
Might the modifications of the vdwradii.dat be suitable for such
system expanding or (on other hand) reduction (as in the below picture
are shown). In the lattter case I defined new box dimensions (smaller
than initial box dims) and would
Thanks Tsjerk,
In my system, I need to model one of the TYR side chains in radical
form. Now while doing that I need to get proper charges as you said.
According I have calculated the ESP charges in Gaussian for the TYR
radical [ unprotonated,neutral, terminals are capped with -NMe and
-COCH3] .
Hi all,
I want to insert a protein in POPC lipid bilayer.
First of all, I simulated POPC in water in 310 K. Now, I want to insert protein
in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300
K and then go on. Does anybody know it would be incorrect logically ?
You should do NVT equilibration to your target temperature. Your system is
already heavily changed between the equilibrated full bilayer and the
embedded protein system so velocities will be reassigned anyway.
On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote:
Hi all,
I want to insert
On 10/3/12 9:39 AM, Shima Arasteh wrote:
Hi all,
I want to insert a protein in POPC lipid bilayer.
First of all, I simulated POPC in water in 310 K. Now, I want to insert protein
in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300
K and then go on. Does
I see that the velocities will be reassigned, but what I'm concerned about, is
reporting the results in a paper. How would it be?
Thanks for your suggestion Peter.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Discussion list for GROMACS users
On 10/3/12 9:57 AM, Shima Arasteh wrote:
I see that the velocities will be reassigned, but what I'm concerned about, is
reporting the results in a paper. How would it be?
That all depends on the answers to my previous questions, as well as the
following: why did you simulate the protein
Hello Emanuel.
First of all thank you for your help. I am sorry if my previous e-mail was a
bit confusing. I will tell what I did recently.
(1) I removed all the information :molecule type, atoms, bonddihedral from
my top file and pasted them to the ipt file , the one I called
It sounds like you want to report that you created a bilayer, equilibrated it
at 310K then inserted the protein and ran MD of the embedded system at 300K?
On 2012-10-03 06:57:22AM -0700, Shima Arasteh wrote:
I see that the velocities will be reassigned, but what I'm concerned about,
is
On 10/3/12 10:03 AM, Elie M wrote:
Hello Emanuel.
First of all thank you for your help. I am sorry if my previous e-mail was a
bit confusing. I will tell what I did recently.
(1) I removed all the information :molecule type, atoms, bonddihedral from my
top file and pasted them to the
Actually, I want to study this system of protein-membrane, trying to replicate
in vitro conditions and then studying function of the protein.
I simulated the protein in water to see the usual result : losing its native
configuration. Then, I am trying to insert the protein in membrane to study
yes, that's right.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Wednesday, October 3, 2012 5:37 PM
Subject: Re: [gmx-users] Temperature in simulation
It sounds like you want to report that
Justin,
thanks for advises.
Finally how I could effectively reduce size of my system (in x and y )
to the defined pbc box size ( see picture to the previous comment) ?
I've noticed that increasing of x and y to the 12 nm I obtain ideal
shape of the bilayer without miss-matches of the left and
On 10/3/12 12:38 PM, James Starlight wrote:
Justin,
thanks for advises.
Finally how I could effectively reduce size of my system (in x and y )
to the defined pbc box size ( see picture to the previous comment) ?
I've noticed that increasing of x and y to the 12 nm I obtain ideal
shape of
On 10/3/12 10:16 AM, Shima Arasteh wrote:
Actually, I want to study this system of protein-membrane, trying to replicate
in vitro conditions and then studying function of the protein.
I simulated the protein in water to see the usual result : losing its native
configuration. Then, I am
You are right and I will insert the native protein in membrane. To do so, I
want to set the temperature of nvt.mdp file to 300 K, however I want to use the
result output of memrane simulated in 310 K for 50 ns.
Through your earlier suggestions, I got that velocities would be reassigned in
new
On 10/3/12 2:02 PM, Shima Arasteh wrote:
You are right and I will insert the native protein in membrane. To do so, I
want to set the temperature of nvt.mdp file to 300 K, however I want to use the
result output of memrane simulated in 310 K for 50 ns.
Through your earlier suggestions, I got
Dear Gromacs users,
I would like to simulate water on Ruthenium surface. Would you please suggest
the force field used to describe Ru.
Many thanks.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
On 10/3/12 5:17 PM, Ho, Tuan A. wrote:
Dear Gromacs users,
I would like to simulate water on Ruthenium surface. Would you please suggest
the force field used to describe Ru.
You're not likely to find one built into Gromacs by default.
Sorry it seems that those breaks are due to hotmail and not present in the
topology. Thanks for your reply. I still have problems...I will tell u briefly
and as clear as possible what i did.
(1) My top file has the following lines ate first:
; Include forcefield parameters #include
Thanks
On Wed, Oct 3, 2012 at 6:04 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/3/12 12:06 AM, naga sundar wrote:
Dear Pramod
use the command
xmgrace -nxy file1.xvg file2.xvg
Instead of file1 and file2 use ur file name.
On 10/3/12 7:48 PM, Elie M wrote:
Sorry it seems that those breaks are due to hotmail and not present in the
topology. Thanks for your reply. I still have problems...I will tell u briefly
and as clear as possible what i did.
(1) My top file has the following lines ate first:
; Include
On 10/3/12 10:43 PM, Nur Syafiqah Abdul Ghani wrote:
Dear Users,
Right now i already done for creating the a gro file from antechamber
to gromacs format of my molecule which is hexafluoroisopropanol.
But when i want to minimize it in vacuum it show atomtype F not found.
Im using oplsaa force
Hi Deepak,
Is the gromacs is in your path??
Please mention your operating system..
With best wishes and Regards,
rama david
On Thu, Oct 4, 2012 at 11:07 AM, Deepak Ojha alwaysinthem...@gmail.comwrote:
Dear All
I want to use Amber force field in Gromacs therefore I installed the
latest
Justin,
lastly, is there any other ways to obtain bilayers of desired
dimensions started from just one lipid oriented in desired way for
instance?
James
2012/10/3, Justin Lemkul jalem...@vt.edu:
On 10/3/12 12:38 PM, James Starlight wrote:
Justin,
thanks for advises.
Finally how I
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