hello Mar:
thanks a lot for kind reply.
From the link you you mentioned, it seems that this problem comes
from the MD system itself. However, it goes well in my workstation.
Moreover, I visualized and analyzed the results from my workstation
running, everything goes well. I don't find any
hello Makr:
thanks a lot for kind reply.
From the link you you mentioned, it seems that this problem comes
from the MD system itself. However, it goes well in my workstation.
Moreover, I visualized and analyzed the results from my workstation
running, everything goes well. I don't find any
Hi.
I am trying to the the PMF of transferring a drug molecule from the aqueous
phase to a lipid bilayer.
In order to minimize the effects of membrane undulations I tried to use
pull_geometry=cylinder.
Whenever I run a short simulation with umbrella sampling starting from a
configuration with
Dear All,
Will you please tell me a method or a server which can calculate the mean B
factor of all residues in a PDB file?
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
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Dear Gromacs Users!
I have a model of my protein wich has 4 S-S bounds in the loop regions. So
I want to define in topology all those four S-S linkage.
Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also
I've tried to check this bond in pymol and found that distance between
Hi James,
usually people run a minimization using distance restrain on the two atoms
in order to
make them closer.
Then the obtained cnfiguration is used to recalculate the topology.
Francesco
2012/4/28 James Starlight jmsstarli...@gmail.com
Dear Gromacs Users!
I have a model of my protein
Hi Francesco!
So I must define in the current topology the disres bettwen two S atoms (
in the below example 1 and 10 ) to apply hormonic restains
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1 10 10 10.18 0.20 0.22 1.0
to restrain this atoms within 0.2 nm.
On 4/28/12 5:41 AM, Acoot Brett wrote:
Dear All,
Will you please tell me a method or a server which can calculate the mean B
factor of all residues in a PDB file?
A simple script to parse out the B-factor field and calculate the average should
do the trick.
-Justin
--
On 4/28/12 5:12 AM, J B wrote:
Hi.
I am trying to the the PMF of transferring a drug molecule from the aqueous
phase to a lipid bilayer.
In order to minimize the effects of membrane undulations I tried to use
pull_geometry=cylinder.
Whenever I run a short simulation with umbrella sampling
Hello Everyone,
I am trying to pull ligand biotin out of the streptavidin protein.Following
the tutorial Protein ligand complex by Justin ,i have done till energy
minimization step skipping adding solvent and ion step,and skipping
pressure and temperature equilibration.Now how to proceed further
On 28/04/2012 4:14 PM, Albert wrote:
hello Mar:
thanks a lot for kind reply.
From the link you you mentioned, it seems that this problem comes
from the MD system itself. However, it goes well in my workstation.
Moreover, I visualized and analyzed the results from my workstation
running,
.. and the main question- what should be in mdp file of such restrained
minimisation ?
Today I've done vry properly minimisation of such system in vacuum with the
CG minimisator and applied disres ( above example ) with big force constant
( disres options have been defined in the minim.mdp file
Hi James,
usually I insert by hand a bond in the topology file between the two
atoms and then I minimize.
This bond doesn't cause the generataion of angles and dihedrals, butit
is enough to make the atom closer.
Francesco
Il 28/04/2012 16:08, James Starlight ha scritto:
.. and the main
On 4/28/12 10:08 AM, James Starlight wrote:
.. and the main question- what should be in mdp file of such restrained
minimisation ?
Today I've done vry properly minimisation of such system in vacuum with the CG
minimisator and applied disres ( above example ) with big force constant (
disres
Francesco,
Thanks, I find your aproach very handfull :)
Justin,
in that example I've defined in minim.mdp
*disre = simple
**disre_f = 5000
in the topology.top I've included
* [ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1 10 10 10.18 0.20 0.22 1.0
On 4/28/12 10:25 AM, James Starlight wrote:
Francesco,
Thanks, I find your aproach very handfull :)
Justin,
in that example I've defined in minim.mdp
This would have been useful to state up front. Your previous question implied
that you didn't know if any special keywords were
Hi,
the distance is 3.89 nm and the z-dimension is roughly 8 nm
Date: Sat, 28 Apr 2012 09:18:31 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with
pull_geometry=cylinder
On 4/28/12 5:12 AM, J B wrote:
Hi,
Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you
know, automatic threading is awesome because it allows me to start parallel
runs without calling mpirun. So on version 4.5.5, I can start a job on eight
CPUs using simply the command:
mdrun -s topol.tpr -nt 8
However,
oops I meant /usr/local/gromacs/bin in PATH
also 4.5.4 has support for threading if compiled that way...Most clusters don't
use it because nodes on separate chassis usually don't support shared memory
with each other. We get really bad performance when using
threading-over-scalemp as compared
Dear gmx users,
I want to simulate POPC in water. In equilibration step, I have to make an
index file. But when I enter this command, I do not know to choose which group
to make a suitable .ndx file which matches the molecule types and molecules
sections in .top file .
The .top file contains
#2
Generally a good idea to keep the names consistent, however - why are you using
POP in the coordinate file instead of POPC?
--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
Shima Arasteh shima_arasteh2...@yahoo.com wrote:
Dear gmx users,
I want to simulate POPC in
On 4/28/12 2:06 PM, Peter C. Lai wrote:
#2
Generally a good idea to keep the names consistent, however - why are you using
POP in the coordinate file instead of POPC?
If it is a .pdb file, the standard residue name occupies 3 characters. Many
files (including those from Tieleman) are
On 4/28/12 12:28 PM, J B wrote:
Hi,
the distance is 3.89 nm and the z-dimension is roughly 8 nm
Is the problem specific to cylinder geometry? Do other settings work? Does it
make a difference if you set values for pull_r0 and pull_r1?
-Justin
Date: Sat, 28 Apr 2012 09:18:31
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