Hi
do the following ..
open the trajectory in tthe molecule not as seperate molecule..
As example you havre md.gro and md.xtc files..
file == new molecule
load files for md.pdb open it in vmd ..
then be sure that load files for : sould have the file name for which
you want to see
Sorry md.pdb/md.gro
On Thu, Aug 16, 2012 at 11:34 AM, rama david ramadavidgr...@gmail.com wrote:
Hi
do the following ..
open the trajectory in tthe molecule not as seperate molecule..
As example you havre md.gro and md.xtc files..
file == new molecule
load files for md.pdb open it in
Hi Mark,
Thanks for your previous reply.
I tried to run single point energy simulation with some proteins.
I got .log files with content like this:
Energies (kJ/mol)
Bond AngleProper Dih. Improper Dih.GB Polarization
1.54109e+043.84351e+038.47152e+03
On 16/08/2012 4:26 PM, jesmin jahan wrote:
Hi Mark,
Thanks for your previous reply.
I tried to run single point energy simulation with some proteins.
I got .log files with content like this:
Energies (kJ/mol)
Bond AngleProper Dih. Improper Dih.GB Polarization
Hi Mark,
Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the the bonded terms and zero the VDW parameters?
I really need to compare how fast different well known package can
compute GB-polarization energy and how good the energy
On 16/08/2012 5:08 PM, jesmin jahan wrote:
Hi Mark,
Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the the bonded terms and zero the VDW parameters?
In the .top file from which you made the .tpr. (And contributing .itp
files)
Hi Sébastian,
I think the magic word in this issue would be surface tension and the
proper ensemble for the simulation NPgammaT. This is very well discussed
in the paper I advised to you a couple of days ago. The issue is by no
means trivial, although I'm not an expert to judge it. You can
Thank you so much for your time and explanation.
I am recalculating the energy co-ordinates and using it in g_lie
calculations.
I have read the manual and changed the .mdp file I am using. The following
is the mdp file, please check for the correctness. The text in bold font are
newly included
I think the confusion arises form
15 aug 2012 kl. 22.53 skrev Justin Lemkul:
On 8/15/12 4:49 PM, Andrew DeYoung wrote:
Hi,
I am a novice user of g_hbond (actually, I am using double precision --
g_hbond_d -- but I think all of the parameters should be the same).
I would like to use
Hi,
I think the confusion arises from how the xpm data is displayed. If you have
the hb-index on the y-axis in a plot with the positive y-direction pointing
upwards (as in most plots), then the first line in the xpm file is actually
displayed at the bottom. For matrices, however, the indexing
Dear Mark,
Once again I am very thankful to you for your reply, I
have extracted box vectors from .XTC file by using g_traj with -ob
option with this I was able to get only six vector components viz XX
YY ZZ YX ZX and ZY only how about remaining three vector components
XY XZ
Dear justin Thank you for your gem of Reply
I am doing ED. With respect to my all 900 C-alpha atoms
So I have used the output of g_covar namely eigvec.trr as input to g_anaeig_d
as follows
g_anaeig_d -v eigenvec.trr -comp eig1.xvg -first 1 -last 3 -xvg none
I have obtained eig1.xvg i
Dear all,
I have a 70 ns trajectory for which the last 60 ns appears to be
equilibrated. I'm attempting to create a plot of RMSF but I want to align
it to the equilibrated structure, not the starting structure. I first ran
g_rmsf using the starting structure as the reference structure over only
Dear All,
In my simulation I want the temperature of the system to be reached at
300 K only after 3 ps. But after 3ps I see temperature became 402 K.
So am I doing any mistake in the '.mdp' file given below?
define= -DFLEXIBLE
constraints= h-bonds
integrator = sd
On 8/16/12 10:13 AM, tdgrant1 wrote:
Dear all,
I have a 70 ns trajectory for which the last 60 ns appears to be
equilibrated. I'm attempting to create a plot of RMSF but I want to align
it to the equilibrated structure, not the starting structure. I first ran
g_rmsf using the starting
On 8/16/12 12:57 PM, tarak karmakar wrote:
Dear All,
In my simulation I want the temperature of the system to be reached at
300 K only after 3 ps. But after 3ps I see temperature became 402 K.
So am I doing any mistake in the '.mdp' file given below?
You have a few.
1. You should not run
Thanks a lot for the quick reply...probably I have
overlooked this point earlier
..now I'm getting it properly
On Thu, Aug 16, 2012 at 10:33 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/16/12 12:57 PM, tarak karmakar wrote:
Dear All,
In my simulation I
Dear Gromacs Users,
I am trying to simulate a modeled protein -ligand complex in lipid
bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose
which is to see the effect of substitution of ions (Ca instead of Na
ions) in the protein structure on protein ligand interactions , I
have
On 8/16/12 2:45 PM, ram bio wrote:
Dear Gromacs Users,
I am trying to simulate a modeled protein -ligand complex in lipid
bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose
which is to see the effect of substitution of ions (Ca instead of Na
ions) in the protein structure on
Hi Justin,
I did indeed correct for periodic boundary conditions prior to running rmsf,
so I'm not sure what the problem would be there.
Is there any way of producing an average structure from rmsf (or any other
program for that matter) that is not output as a .pdb file but as a .tpr
file?
On 8/16/12 3:19 PM, tdgrant1 wrote:
Hi Justin,
I did indeed correct for periodic boundary conditions prior to running rmsf,
so I'm not sure what the problem would be there.
The message you got was a warning, not an error. The warning is generic and is
printed by any Gromacs program that
Oh okay, thanks. I didn't realize warnings were just that, only warnings and
didn't stop the program. The program did not finish however, and the
problem was a Segmentation Fault. The output literally was:
Select a group: 0
Selected 0: 'System'
Reading frame 0 time0.000
WARNING:
On 8/16/12 3:54 PM, tdgrant1 wrote:
Oh okay, thanks. I didn't realize warnings were just that, only warnings and
didn't stop the program. The program did not finish however, and the
problem was a Segmentation Fault. The output literally was:
Select a group: 0
Selected 0: 'System'
Reading
This System as described by group 0 in the previous message is actually
only the solute, a protein-tRNA complex of ~15000 atoms. I tried running
only the backbone and even only c-alphas (808 atoms total) and I still
received a segmentation fault.
--
View this message in context:
On 8/16/12 4:11 PM, tdgrant1 wrote:
This System as described by group 0 in the previous message is actually
only the solute, a protein-tRNA complex of ~15000 atoms. I tried running
only the backbone and even only c-alphas (808 atoms total) and I still
received a segmentation fault.
Do the
No they do not. The trajectory contains all the atoms, including the solvent
(~300,000 atoms), whereas the structure passed to -s is the averaged
structure from the last 60ns of simulation and only includes the non-solvent
atoms (~15,000). Should I rerun rmsf on the last 60ns but select System
On 8/16/12 4:19 PM, tdgrant1 wrote:
No they do not. The trajectory contains all the atoms, including the solvent
(~300,000 atoms), whereas the structure passed to -s is the averaged
structure from the last 60ns of simulation and only includes the non-solvent
atoms (~15,000). Should I rerun
Dear All,
I have bilayer system plus two proteins in my system. I numbered residues
manually, but after minimization number of residues for both protein 1 and 2
starts from 1. It means in VMD when I am going to pick res. 3 (resid 3), it
will highlight two res. 3, one in protein 1 and one in
On 8/16/12 5:22 PM, dariush wrote:
Dear All,
I have bilayer system plus two proteins in my system. I numbered residues
manually, but after minimization number of residues for both protein 1 and 2
starts from 1. It means in VMD when I am going to pick res. 3 (resid 3), it
will highlight two
Hi,
I have a question about the Protein-POPC system:
To insert a protein in lipid bilayer, I am suggested to simulate POPC in water
separately before insertion, it might decrease the time of final simulation.
It's OK!
In the article suggested me by dear Peter C. Lai, I read that POPC was
After inserting the protein, the equilibrium box length in the x and y
dimension should be different, so you need anisotropic pressure coupling during
the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so
you can use semi-isotropic method.
--Jianguo
On 8/16/12 9:14 PM, Jianguo Li wrote:
After inserting the protein, the equilibrium box length in the x and y
dimension should be different, so you need anisotropic pressure coupling during
the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so
you can use
What I think is that anisotropic coupling may be
faster in equilibrium. Suppose the protein is quite different in x and y
dimensions, after insertion, I think it is faster to get equilibrium
the box length separately. I agree with you that semi-isotropic coupling in the
first step can also do
On 8/16/12 9:43 PM, Jianguo Li wrote:
What I think is that anisotropic coupling may be faster in equilibrium. Suppose
the protein is quite different in x and y dimensions, after insertion, I think
it is faster to get equilibrium the box length separately. I agree with you that
semi-isotropic
On 17/08/2012 11:46 AM, Justin Lemkul wrote:
On 8/16/12 9:43 PM, Jianguo Li wrote:
What I think is that anisotropic coupling may be faster in
equilibrium. Suppose
the protein is quite different in x and y dimensions, after
insertion, I think
it is faster to get equilibrium the box length
You always use semi-isotropic for bilayer work. The Z is decoupled from x-y
due to symmetry.
I don't think I mention anything differently in the paper.
Pcoupltype = semiisotropic
On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
Hi,
I have a question about the
On 8/16/12 10:21 PM, Mark Abraham wrote:
On 17/08/2012 11:46 AM, Justin Lemkul wrote:
On 8/16/12 9:43 PM, Jianguo Li wrote:
What I think is that anisotropic coupling may be faster in equilibrium. Suppose
the protein is quite different in x and y dimensions, after insertion, I think
it is
Here is my MDP file I use for POPC work for NPT-after-NVT equilibration,
in caes you lost it from the time before:
You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
Parinello-Rahman with the paraeters below was stable for me with 238 POPC
and 21524 water.
integrator
Not directly related to bilayers, but our work with liquid phases has found
some interesting things with anisotropic versus isotropic. Basically, even
though anisotropic allows things to structure without constraints to how they
want to be, there is some artifacts that drive it too far, beyond
Hi Mark,
According to your advice remove the the bonded terms and zero the
VDW parameters,
I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
], and run the simulation mdrun rerun.
I got output something like the following:
Energies (kJ/mol)
GB PolarizationLJ
In 2.1.6. Membrane bilayer construction part of the article you mentioned:
Asingle POPC molecule is parameterized using a
CHARMM36 force field conversion for GROMACS7. The result-
ing system,which consists of around 238 lipids is then equilibrated
for at least 50 ns at 310 K and 1 atm under NPT
Can't remember why I said that, since it's not what I used. Stupid
autocorrect? Sorry!
On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
In 2.1.6. Membrane bilayer construction part of the article you mentioned:
Asingle POPC molecule is parameterized using a
CHARMM36 force field
On 17/08/2012 1:14 PM, jesmin jahan wrote:
Hi Mark,
According to your advice remove the the bonded terms and zero the
VDW parameters,
I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
],
This only removes the bonded terms (in the sense of those atoms that
interact
Dear all
One basic clarification. How does LINCS algorithm influences the results
of final production run. In what respect a minimization, pr and final
simulation done with constraints = none and with constraint= all_bonds are
different.
Shahid Nayeem
--
gmx-users mailing list
Oh, It's OK. Thanks Peter. :-)
I used the the same .mdp file sent me by you 1 month ago, for the
pre-equilibration of POPC in water.
But as others said here, anisotropic pressure coupling might result in major
changes in lipid bilayer. I don't know, but it seems it is better to use
On 17/08/2012 2:02 PM, shahid nayeem wrote:
Dear all
One basic clarification. How does LINCS algorithm influences the results
of final production run. In what respect a minimization, pr and final
simulation done with constraints = none and with constraint= all_bonds are
different.
Sounds like
On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote:
Oh, It's OK. Thanks Peter. :-)
I used the the same .mdp file sent me by you 1 month ago, for the
pre-equilibration of POPC in water.
Well if that worked out, then what is the problem?
What do you mean by pre-equlibration The only
:-)
Thanks Peter.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, August 17, 2012 8:48 AM
Subject: Re: [gmx-users] Protein-POPC bilayer
On
Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy minimization with setting constraint =
none, making it
On 17/08/2012 2:28 PM, shahid nayeem wrote:
Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy
I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
Shahid nayeem
On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 17/08/2012 2:28 PM, shahid
On 17/08/2012 2:56 PM, shahid nayeem wrote:
I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
All you can do is use pdb2gmx as you do for the normal termini. pdb2gmx
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