users gmx-users@gromacs.org
Sent: Thursday, August 22, 2013 6:37 PM
Subject: Re: [gmx-users] position restraint
Now you have a [moleculetype] with one atom and hopefully a position
restraint. But its [position_restraints] wants to act on atom 85563 of
the molecule, which does not exist! See newly
Hi,
I want to put position restraint on an ion ,
First made an .itp file of the ion: posre_ion.itp
Then added these line to top file:
#include ./charmm36-modified.ff/ions.itp
#ifdef POSRES_ION
#include ion_posre.itp
#endif
And added the line to mdp file
define = -DPOSRES_ION
But the
One quick observation-- you mention the filename as posre_ion.itp, but are
using ion_posre.itp at #include. -g
On Thu, Aug 22, 2013 at 4:24 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Hi,
I want to put position restraint on an ion ,
First made an .itp file of the ion:
:39 PM
Subject: Re: [gmx-users] position restraint
One quick observation-- you mention the filename as posre_ion.itp, but are
using ion_posre.itp at #include. -g
On Thu, Aug 22, 2013 at 4:24 PM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
Hi,
I want to put position restraint
On 8/22/13 7:13 AM, Shima Arasteh wrote:
yes, but there was only a typing mistake in my earlier email.
Always copy and paste; don't re-type.
The error I get still exists when I use the correct itp file:
First made an .itp file of the ion: ion_posre.itp
Then added these line to top
: [gmx-users] position restraint
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
I want to put position restraint on an ion ,
First made an .itp file of the ion: posre_ion.itp
Then added these line to top file:
#include ./charmm36-modified.ff/ions.itp
#ifdef POSRES_ION
#include
with it please?
Sincerely,
Shima
-- Forwarded message --
From: Shima Arasteh shima_arasteh2...@yahoo.com
Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT)
Subject: [gmx-users] position restraint
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
I want to put position
shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Thursday, August 22, 2013 5:54 PM
Subject: Re: [gmx-users] position restraint
Have a look at that file. It defines the [moleculetype] for lots of
ions, but you need a position restraint that applies to whichever
Message -
From: Mark Abraham mark.j.abra...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Thursday, August 22, 2013 5:54 PM
Subject: Re: [gmx-users] position restraint
Have a look at that file. It defines
-
From: Mark Abraham mark.j.abra...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, August 22, 2013 6:37 PM
Subject: Re: [gmx-users] position restraint
Now you have a [moleculetype] with one atom and hopefully
Dear users and developers:
We have conducted some NPT umbrella sampling (US) simulations to investigate
the free energy associate with the aproach of 2 alpha helical peptides. The
order parameter is the Cartesian X dimension. During these simulations, in
order to maintain (i) the structure of
Hi gmxusers,
Hope you are well. I am trying to apply position restraints to my crystal
waters (just briefly, 1-2ns) but have been unsuccessful.
Taking into account the advice from this thread
http://lists.gromacs.org/pipermail/gmx-users/2012-February/068780.html, this
was what I had done:
Dear Gromacs users:
I am trying to extract the constraint energy imposed by position restraint.
I extract the coordinate of the restraint atom and want to calculated
directly by using the harmonic potential. The question is : Does the
reference position come from the .gro file as the input in
Dear Gromacs Users,
Harmonic potentials are used in Gromacs for imposing restraints on the
motion of the system.
V = 1/2 * k * (x-x0)^2
And the forces are : F = -k * (x-x0) . ...
I want to use constant force for the restraint.
Just scale the force : F = -k * (x-x0)
Dear Gromacs Users,
Harmonic potentials are used in Gromacs for imposing restraints on the
motion of the system.
V = 1/2 * k * (x-x0)^2
And the forces are : F = -k * (x-x0) . ...
I want to use constant force for the restraint.
Just scale the force : F = -k * (x-x0)
On 10/07/2011 9:01 PM, chicago.ecnu wrote:
Dear Gromacs Users,
Harmonic potentials are used in Gromacs for imposing restraints on
the motion of the system.
V = 1/2 * k * (x-x0)^2
And the forces are : F = -k * (x-x0) . ...
I want to use constant force for the restraint.
Just
Thank you Justin and Mark for your help. The problem is that I wasn't
using the .gro file from the minimization step and it was giving a
segmentation fault problem too, but I've corrected that problem, ran the
simulated annealing without constraints and it worked fine.
But I have another
On 18/01/2011 10:01 AM, Marcelo Silva wrote:
Thank you Justin and Mark for your help. The problem is that I wasn't
using the .gro file from the minimization step and it was giving a
segmentation fault problem too, but I've corrected that problem, ran
the simulated annealing without constraints
Hello everybody,
I tried to run a simulated annealing protocol with 500 molecules of
perfluorohexane, trying to optimize their structure and keep on with further
equilibration.
Since in the end of simulated annealing there were a lot of holes in the NPT
box, I've now tried to restrain the
Marcelo Silva wrote:
Hello everybody,
I tried to run a simulated annealing protocol with 500 molecules of
perfluorohexane, trying to optimize their structure and keep on with
further equilibration.
Since in the end of simulated annealing there were a lot of holes in the
NPT box, I've now
On 17/01/2011 6:25 AM, Marcelo Silva wrote:
Hello everybody,
I tried to run a simulated annealing protocol with 500 molecules of
perfluorohexane, trying to optimize their structure and keep on with
further equilibration.
Since in the end of simulated annealing there were a lot of holes in
nikhil damle wrote:
Hey !
My doubt posted few days back still holds. I am trying to simulate the
kinase domain in complex with cyclin. when i keep entire complex either
position restrained or flexible, MD runs without any errors. But as soon
as i keep cyclin position restrained keeping
Hey !
My doubt posted few days back still holds. I am trying to simulate the kinase
domain in complex with cyclin. when i keep entire complex either position
restrained or flexible, MD runs without any errors. But as soon as i keep
cyclin position restrained keeping kinase domain flexible, it
Hi,
I am trying to reproduce some steps from a paper, the authors set position
restraint to the protein (all-bonds) with a force constant of 1000 for 2ns.
I edited the pr.md file where nsteps would result in 2 ns, and I searched the
mailing list and knew that the force cons is 1000 by default
Rabab Toubar wrote:
Hi,
I am trying to reproduce some steps from a paper, the authors set
position restraint to the protein (all-bonds) with a force constant of
1000 for 2ns.
Constraints and restraints are different things in Gromacs, so setting position
restraints is done independently
Dear gmx-users,
I am trying to create a tpr file using grompp. My system has a protein with
four identical chains, 288 POPC molecules, SOL, and ions. I am trying to
restrain the lipid molecules. When running grompp, I get the following
message:
Program grompp, VERSION 3.3
Source code file:
On Jul 28, 2009, at 9:50 AM, Morteza Khabiri wrote:
Dear gmx-users,
I am trying to create a tpr file using grompp. My system has a
protein with
four identical chains, 288 POPC molecules, SOL, and ions. I am
trying to
restrain the lipid molecules. When running grompp, I get the
Hi..dear gromacs users...How do we decide the ideal time to run PR??we are
simulating a protein of 260 amino acids which is a tirmer...we have done
the PR for 10 ps first time and 100ps for the second ...i had observed a
stable graph in the latter compared with the other...and on what factors
bhargavi ch wrote:
Hi..dear gromacs users...How do we decide the ideal time to run PR??we
are simulating a protein of 260 amino acids which is a tirmer...we have
done the PR for 10 ps first time and 100ps for the second ...i had
observed a stable graph in the latter compared with the
Hi
we are simulating a protein of 260 a.a length which is a trimer...How does
the mdrun time during the position restraint dynamics affects the Full
Dynamics results???
Regards
Bhargavi
___
gmx-users mailing listgmx-users@gromacs.org
If you want to know how much time is required for this step (assuming
that this step is even required) then that is system dependent and
something that you would ideally test for yourself. For example, after
N ps of position restrained dynamics, how does that affect the RMSD of
the protein
Hi,
Yes. You can use GROMACS to simulate traffic if you want to. :-)
Mark, do you have a force field for that?
As i had done it with 4 residue with blocking group. But then i got the
error for rvdw and rlist as they should be nearer to cutoff value.
So instead of decreasing the value of
Tsjerk Wassenaar wrote:
Hi,
Yes. You can use GROMACS to simulate traffic if you want to. :-)
Mark, do you have a force field for that?
Nah, parameterization against experimental data is really expensive.
Mark
___
gmx-users mailing list
hello everyone,
pls tell me that whether we can use gromacs for simulating pdb with 3 or 4
residue.
As i had done it with 4 residue with blocking group. But then i got the
error for rvdw and rlist as they should be nearer to cutoff value.
So instead of decreasing the value of rvdw. i increased my
Bhawana Gupta wrote:
hello everyone,
pls tell me that whether we can use gromacs for simulating pdb with 3 or
4 residue.
Yes. You can use GROMACS to simulate traffic if you want to. :-)
As i had done it with 4 residue with blocking group. But then i got the
error for rvdw and rlist as
Hi,
For some reasons, I want to try to simulate a nanotube not as an ordinary
molecule (with intramolecular potentials, etc) but as a group of
sternly fixed single carbon atoms (also energygrp_excl = UNK UNK).
In topology:
; carbon positio restraint
[ position_restraints ]
111000 1000
*hi!
I am attempting to run a distance position restrained simulation in water.
The **distance and position restraining files are called from the *.top file
as posres.itp and disres.itp. After a 200ps run I do not see the distance
nor position restraining kicking in. I am not sure if I have
jayant james wrote:
hi!
I am attempting to run a distance position restrained simulation
in water. The distance and position restraining files are
called from the *.top file as posres.itp and disres.itp. After a 200ps
run I do not see the distance nor position restraining kicking in. I am
not
Dear users,
How can I restrain a certain atoms on a plane?
For example, I want to restrain phosphurus atoms of lipid molecules at z=1.0nm.
Is there a way to do this?
--
Best wishes,
MYUNGGI YI
==
KLB 419
Institute of Molecular Biophysics
Florida State
Myunggi Yi wrote:
Dear users,
How can I restrain a certain atoms on a plane?
For example, I want to restrain phosphurus atoms of lipid molecules at
z=1.0 nm.
Is there a way to do this?
You can either freeze in one dimension or position restrain to a plane,
by setting the force constants
Thank you.
I'm a beginner.
How can I setup the restrain?
Where should I get the information.
The manual is not enough for me.
The position restraint .itp file dosen't seem to offer for the reference (z=
1.0) option.
Whould give me more detail?
On Jan 16, 2008 3:14 PM, David van der Spoel [EMAIL
check
http://wiki.gromacs.org/index.php/Position_Restraints
___
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post
Where should I put z=1.0 ?
On Jan 16, 2008 3:22 PM, Anirban Mudi [EMAIL PROTECTED] wrote:
check
http://wiki.gromacs.org/index.php/Position_Restraints
___
gmx-users mailing listgmx-users@gromacs.org
Thank you.
I've already read the part, but I was wondering how can I supply my
reference z positon in the .itp file.
I can prepare the restraint.gro file manually by placing the atoms at z=
1.0 nm.
Then I think I can supply with -r option.
Have a great day.
On Jan 16, 2008 3:44 PM, Mark
Quoting Myunggi Yi [EMAIL PROTECTED]:
Thank you.
I've already read the part, but I was wondering how can I supply my
reference z positon in the .itp file.
You don't. If you read the link that was provided earlier, or the manual, as
has been suggested, you will find that posre.itp does not
On Wed, 16 Jan 2008 16:12:23 -0500
Justin A. Lemkul [EMAIL PROTECTED] wrote:
Quoting Myunggi Yi [EMAIL PROTECTED]:
Thank you.
I've already read the part, but I was wondering how can I supply my
reference z positon in the .itp file.
There are no direct way to restrain an atom to stay a a
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