Hello,
I am trying to make an dynamic index file of the hydration shell of my
protein (hopefully using it with other gromacs tools). I am considering
up to 10A from protein as the distance needed for my selection.
I am using g_select with the following format:
g_select -f traj.xtc -s traj.tpr -on
Hi,
I used g_select to choose the hydration shell molecules of my protein
from a trajectory of 15ns saved every 10ps (1500 frames). Now I want to
feed the generated index file into g_spatial to calculate the SDF of
solvent around my protein. However, when I feed this into the g_spatial,
it lists
Hello,
My take on g_rotacf is that calculates the correlation times for a
globular proteins that basically the moments of inertia can be assumed
to be the same in all directions. Then, a single diffusion constant can
be calculated for the whole protein. What if your protein is for
instance a
Hello,
I am trying to rotate my protein in my simulation box (solvent molecules
are there as well). I issue the following command:
editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15
180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328
I select my group
but it clearly points to input.
All the best
Roman
On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:
Dear Roman,
do_dssp does analysis on secondary structure of proteins. It is written
on online blogs that to get the correct results, you should select alpha
carbons, option 3. However
Dear Justin,
Thanks a lot. Your comment was very instructive. So, I use Mainchain
(group 5) for future.
Paymon
On Wed, 2010-10-06 at 12:41 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
Hello,
To investigate the secondary structure I issued the do_dssp command as
follows
Hello,
I want to check the secondary structure of protein at particular residues.
Since dssp needs all main chain atoms, does the following command at the
make_ndx prompt makes the correct index file?
5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
(Main chain atom of particular
:
Paymon Pirzadeh wrote:
Hello, I want to check the secondary structure of protein at particular
residues. Since dssp needs all main chain atoms, does the following command
at the make_ndx prompt makes the correct index file?
You can answer that yourself by looking at the resulting index
suggestions on how we can increase the resolution of
dssp plot and enlarging the axis of residues?
By the way, what would the option -nice do here?
Paymon
On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
Justin,
I produced the index file based on your
Hello,
Can g_densmap produce 2D plots that one axis is the position in box, and
the other is time? In other words, evolution of box content density with
time on either axes of the box?
Regards,
Paymon
--
gmx-users mailing listgmx-users@gromacs.org
,
Paymon
On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote:
On 2010-09-23 20.38, Paymon Pirzadeh wrote:
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
compute the rmsd. something different. I said trjconv.
Paymon
wrote:
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
Paymon
On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some
, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadeh ppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID: 1285178847.11669.66.ca...@paymon-desktop
Content-Type
Hello,
It is said in the mannual that g_order compute the order parameter per
atom for carbon tails. Can it also calculate order (degree of
tetrahedrality) for water molecules if only water oxygens are selected
in index file? The reference paper is for water molecules though. Also,
does it
be a periodic boundary issue, so I issued:
trjconv_d_mpi -f 265K_50_50_50_2.xtc -o 265K_50_50_50_2-pbcfixed -pbc
whole -s 265K_50_50_50_2.tpr
but the problem still persists. Any tips?
Regards,
Paymon
On Tue, 2010-08-31 at 20:37 +0200, David van der Spoel wrote:
On 2010-08-31 20.26, Paymon Pirzadeh
Here is the command:
g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s
265K_50_50_50_2.tpr -o Sg265K
On Tue, 2010-08-31 at 21:15 +0200, David van der Spoel wrote:
On 2010-08-31 21.10, Paymon Pirzadeh wrote:
Yes,
I tried it, but I run into segmentation fault. Here
into the previous segmentation fault.
If I just use the Sg, just the temporal profile is generated which is
not what I want.
Sorry for mass of e-mails, but any tips on that?
Paymon
On Tue, 2010-08-31 at 21:49 +0200, David van der Spoel wrote:
On 2010-08-31 21.19, Paymon Pirzadeh wrote:
Here is the command
Hello,
If we have the .tpr and .xtc outputs, what is the procedure (what
GROMACS utilities should be used) to calculate rotational diffusion
constant of a protein?
Regards,
Paymon
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
Hello,
I have question regarding the execution time of a trajectory. I used to
run my trajectory at 265K or 275K and at the end of the log file the
speed was reported as e.g. 1.18 ns/day. Recently, I changed the
temperature to 288K and now my simulation is not finished in the
assigned wall time
Hello,
This is the second time I am sending this message.
I have a protein which has a few Thr residues on one side of itself. I
would like to know how should I setup mt index file and use which
GROMACS tools to calculate potential energy and Sg of water molecules
that only face these residues as
Hello,
I have a protein which has 4 Thr residues on its one side. I want to
calculate the potential energy and Sg of water molecules these Thr
residues are facing (up to 10 angstrom). I have a 10ns trajectory and I
might need only 5ns of it. How should I set my index file and which
tools will help
Hello,
Is there any links to check or commands to read the xtc,trr and edr
files for our analysis (writing our own scripts)? What are the format of
data in these files for reading them?
Payman
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Hello,
I have a run with the xtc, trr and edr files available. I would like to
color a snapshot of my system with respect to rmsd or potential energy
of my particles. How can I extract the potential energy, rmsd or any
other needed data from the files available? Is there a specific GROMACS
command
Hello,
I like to color my particles in terms of their potential energy, rmsd,
Sg or other properties. Is there a command that can extract such
information from XTC, EDR ot TRR files?
Payman
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Hello,
To restart a run for continuation, which .cpt file should be used? the
one with the outputname.cpt or the outputname_prev.cpt?
Payman
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
?
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: Sunday, November 01, 2009 8:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] trjcat xtc files
Paymon Pirzadeh wrote:
Sorry
to such a strange problem?
On Mon, 2009-11-02 at 18:57 +0100, XAvier Periole wrote:
On Nov 2, 2009, at 18:13, Paymon Pirzadeh ppirz...@ucalgary.ca wrote:
Hi Tom,
Thanks for the tip. It worked on the command line and I had 3000
frames.
But when I fed the file to VMD, it showed only 1800
Hello,
I merged two simulation boxes, and now I want to perform a minimization
to remove the problems at their boundary! I have reduced the dt to
0.1 and emstep to 0.1 as well. But still I get the
message
Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision)
molecule.
Best,
Itamar.
On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote:
Hello,
I merged two simulation boxes, and now I want to perform a
minimization
to remove the problems at their boundary! I have reduced the dt to
0.1 and emstep to 0.1 as well. But still I
Hello,
In a simulation, how is it possible to extract the profiles e.g.
potential as a function of z (coordinate axis of box)?
Payman
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
wrote:
Paymon Pirzadeh wrote:
Hello,
In a simulation, how is it possible to extract the profiles e.g.
potential as a function of z (coordinate axis of box)?
g_potential can do this for electrostatic potential, but I don't know about
anything else. I don't think it is a trivial
Hello,
How can we use the trr file in VMD? I thought since we ask in the mdp
file to output the velocities, then in VMD we should be able to see
molecules colored based on their velocities through the trajectory
options. Am I correct?
Payman
___
I did that but, it did not work! I just get a constant color.
On Sun, 2009-10-11 at 18:27 -0700, Amit Choubey wrote:
yes you can do that by opening the gro file and then loading the .trr
file .
amit
On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh
ppirz...@ucalgary.ca wrote
.
no?
On Sun, 2009-10-11 at 21:37 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
I did that but, it did not work! I just get a constant color.
Unless the velocity is written to a field that VMD recognizes, I don't think
you'll be able to see the velocities colored. For example, VMD
Hello,
I ran an NVT simulation from a minimized configuration. The simulation
ended normally and I have a final configuration as well. But, when I
load the initial coordinates and then I want to add data, which is the
xtc file, nothing happens! no frames are loaded. This is while the xtc
file has
Hello,
Are there any links on how we can merge two simulation boxes to make a
single configuration? What technicalities should be considered?
Payman
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
I have a box of crystal (from another simulation) and a box of solvated
protein. Now I want to put the protein close to my crystal.
Payman
On Fri, 2009-09-18 at 09:04 +1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
Hello,
Are there any links on how we can merge two simulation boxes
of
water. Since a system of water runs just fine, it seems even more likely to
me
that your system is simply crashing immediately, rather than a problem with
Gromacs or the MPI implementation.
-Justin
Paymon Pirzadeh wrote:
Regarding the problems I have on running protein system
Regarding the problems I have on running protein system in parallel
(runs without output), When I run pure water system, everything is fine,
I have tested pure water systems 8 times larger than my protein system.
while the former runs fine, the latter has problems. I have also tested
pure water
I am not sure where things go wrong!
Payman
On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation
+1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of decimal numbers on
computers can be inexact, such that things
:20 +1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
I checked all the force-fields available in the GROAMCS. None of them
have the #2 combination rule which matches my water model! Any
alternatives (rather than changing my water model)?
A water model that isn't compatible with the model
for other users. So, I thought how I
can keep the changes local.
Payman
On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
Hello,
Just a reminder that I had troubled with combination rules between my
water model and GROMACS forcefields. I fixed the problem
I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?
Payman
On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote
:
Paymon Pirzadeh wrote:
I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?
I don't understand what you're saying you've already done
Thanks!
I had misunderstood you! I thought you meant to modify them in the root
directory! My mistake! Thanks a lot. I will try to see what I can do.
Payman
On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
OK! That's fine. But what if I do not have
at 15:45 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
OK! It worked! Thanks a lot again. But I have a final technical
question. After running grompp, it shows that my box has a net charge of
-0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
OK?! or even
atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
This is while I could not find such the mentioned mismatch in the two
files. Should I ignore this warning?
Payman
On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
When I look at the .top
I have tested that if I remove the + sign, grompp will not work at all
and says such molecule does not exists.
So, I am not sure where the Na-NA mismatch comes from?!
Payman
On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
When I look at the .top file
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
Payman
On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
I realized sth about the previous error message I posted
, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of decimal numbers on
computers can
if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!
Payman
On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
Thanks for the tips!
But I still have problem with my added ion. Justin had
wrote:
Paymon Pirzadeh wrote:
Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms
Hello,
I am trying to use a different water model for my proteins (using oplsaa
force field). I use the .itp file which I developed, but pdb2gmx does
not accept it. I am a bit confused on how I can make my water model work
with OPLSaa. Based on what I saw from spc.itp or other samples, do I
need
A. Lemkul wrote:
Paymon Pirzadeh wrote:
Well,
I changed the topology file of the system and manually typed the .itp of
my own water model. Just a reminder that I have used my own water
model's .itp file successfully in pure water systems. This .itp file
starts from [ defaults ] and contains
I checked all the force-fields available in the GROAMCS. None of them
have the #2 combination rule which matches my water model! Any
alternatives (rather than changing my water model)?
Payman
On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
That was very
Hello,
I have a quick question about -shuffle switch in grompp. Do we still
need to apply this option in 4.0.5 when we use parallel versions or
not.
regards,
Payman
___
gmx-users mailing listgmx-users@gromacs.org
Hello all,
A follow up from my previous problems on running the gromacs on glacier
turned out that I had problems in installation. The guide in the manual
was not clear enough. So, I installed the code fine this time, so, I get
errors from 4.0.4 version.
I ran the code interactively on the master
: p.yamin[at]fz-juelich.de
- Original Message -
From: Paymon Pirzadeh ppirz...@ucalgary.ca
Date: Thursday, May 28, 2009 6:35 pm
Subject: [gmx-users] GROMACS on glacier.westgrid.ca
Hello all,
A follow up from my previous problems on running the gromacs on
glacierturned out
60 matches
Mail list logo
