Hello Justin,
Thanks a lot for your reply.
I am using the option freezegrps in my .mdp file, given below:
-
;define = -DSTRONG_POSRES
define =
Amir Marcovitz wrote:
Hi All,
I have some problems with g_wham, and i already gone through all the
postings and didn't find a hint..
basically, I'm trying to calculate PMF between two charged plates.
I've performed a pulling simulation between the 2 plates according to
Justin's UMBRELLA
Dear Gromacs Users
I have set my pull option as constant force and the pull geometry is
distance
the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that
the force applied to the
protein is proportional to the distance between the 2 groups ? else what is
it ?
No, kJ/mol
You could load your gro and trr file into vmd, label the angle, save the
file and plot using excel.
Oly
On 28 April 2010 22:26, Justin A. Lemkul jalem...@vt.edu wrote:
Nilesh Dhumal wrote:
Hello,
I am doing solvation of glucose. I am trying to calculate a angle between
three selected
Hi there,
I'm running a 200ns simulation with a small trisaccharide in water. The
trisacc drifts around the box. I've tried using comm-grps = System and
comm-grps = blank and comm-grps = carb and what is below.
carb is the name I use in my top file and index file. For the index I
specify the
Hi all,
I am using the pre-equilibriated layers from Tieleman. After the first
energy minimization step, I removed the periodicity using trjconv. Now, in
order to scale the lipid positions, I tried using Inflategro.
Do I need to use strong position restraints (because that is for protein and
I am
On Thu, Apr 29, 2010 at 3:29 PM, Saumya samvygu...@gmail.com wrote:
Hi all,
I am using the pre-equilibriated layers from Tieleman. After the first
energy minimization step, I removed the periodicity using trjconv. Now, in
order to scale the lipid positions, I tried using Inflategro.
Do I
Hello Justin,
Thanks a lot for your reply.
I am using the option freezegrps in my .mdp file, given below:
-
;define = -DSTRONG_POSRES
define =
Oliver Grant wrote:
Hi there,
I'm running a 200ns simulation with a small trisaccharide in water. The
trisacc drifts around the box. I've tried using comm-grps = System and
comm-grps = blank and comm-grps = carb and what is below.
Why wouldn't your trisaccharide diffuse around? The only
Anirban Ghosh wrote:
Hello Justin,
Thanks a lot for your reply.
I am using the option freezegrps in my .mdp file, given below:
-
;define =
Respected Sir,
I am trying to generate free energy landscape by using g_sham,From the archive
I came to know that one .xvg file needs to be prepared containing three
columns of data, first one is time, 2nd and 3rd one are the coordinates of
interest, I used the command
g_sham -f *.xvg
Thanks for the help,
With center of mass removal option I thought my sugar would stay in the
center of the box. It does in the first simulation I ran however what I mean
by diffuse is that it leaves the box on one side and enters from the other.
There is nothing physically wrong with this but I'd
Hi again,
I thought your suggestions would work for my membrane, but it seems like the
removal of COM translation of the bilayer and water separately does not stop
the system from translating in the box. My new simulations are now soon
crashing again since the lipids are crossing the pbc. I was
Hi again,
I thought your suggestions would work for my membrane, but it seems like the
removal of COM translation of the bilayer and water separately does not stop
the system from translating in the box. My new simulations are now soon
crashing again since the lipids are crossing the pbc. I was
Hi,
(...)
Output from make:
=
(...)
/bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-
unused -funroll-all-loops -L/usr/local/lib -
framework Accelerate -o grompp grompp.o libgmxpreprocess.la
../mdlib/libmd.la
Oliver Grant wrote:
Thanks for the help,
With center of mass removal option I thought my sugar would stay in the
center of the box. It does in the first simulation I ran however what I
mean by diffuse is that it leaves the box on one side and enters from
the other. There is nothing
Do you have sufficient water on either side of your membrane? That is, are
the lipids crossing PBC because of spurious interactions with the other side of
the membrane? That would certainly be a reason for a crash - the model physics
is breaking down. How did you generate your initial
Hi all,
I have downloaded the latest git version of gromacs (yesterday) in which
it is possible to use the charmm27 force field, I constructed the topology
for my protein using the pdb2gmx program, everything goes ok also with the
solvation, but then when i run the MD i notice that coulomb and LJ
Fabrizio Marinelli wrote:
Hi all,
I have downloaded the latest git version of gromacs (yesterday) in which
it is possible to use the charmm27 force field, I constructed the topology
for my protein using the pdb2gmx program, everything goes ok also with the
solvation, but then when i run the MD
It is indeed not clear how you system may translate still! Is this
translation on
the z axis? How much does it move and how quick?
On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote:
Do you have sufficient water on either side of your membrane?
That is, are the lipids crossing PBC
My system consists of 128 lipids and 3655 water molecules and is one of the
structures one can download from University of Calgary. I think that the water
phase is thick enough because when I run non-constrained simulations and the
system translates there is no crash when the lipids cross the
ERIKSSON, EMMA wrote:
My system consists of 128 lipids and 3655 water molecules and is one of the
structures one can download from University of Calgary. I think that the water
phase is thick enough because when I run non-constrained simulations and the
system translates there is no crash
Thanks for your answers,
I tried to struggle a bit more with that today.
my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and
pullx-files.dat) are fine and consistent with other in terms of file
numbering.
i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler.
i run: *g_wham -it
The last section of my mdp file:
pull = constraint
pull_geometry= cylinder
pull_r1 = 1.0
pull_r0 = 1.5
pull_group0 = DPPC
pull_group1 = MOL
pull_vec1= 0 0 1
pull_init1 = 3.083
- Original Message -
From: J. Rui Rodrigues joaquim.rodrig...@estg.ipleiria.pt
Date: Thursday, April 29, 2010 23:02
Subject: Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
(...)
Output from make:
The translation occurs in the z direction, yes. I'm running many constrained
simulations but in general the movement of the new simulations, in which the
COM translation has been removed for the bilayer and water separately, is about
1 nm in 3 ns. The movement is slower than when I was running
ERIKSSON, EMMA wrote:
The last section of my mdp file:
pull = constraint pull_geometry= cylinder
pull_r1 = 1.0 pull_r0 = 1.5 pull_group0
= DPPC pull_group1 = MOL pull_vec1= 0 0 1
pull_init1
Fabrizio Marinelli wrote:
Here it is my .mdp file, i attach you also the topology file, just to be
more specific the one that are 0 are the SR interactions, thank you very
much.
For diagnostic purposes, can you re-process your structure using a different
force field and try again? If the
The increase in z box length is due to that I have replaced 12 DPPC lipids by
cholesterol molecules. Cholesterol reduces the area per lipid and compresses
the bilayer lateral (xy) area, resulting in a slight increase in the water
layer thickness. I have performed exactly the same simulations
ERIKSSON, EMMA wrote:
The increase in z box length is due to that I have replaced 12 DPPC lipids by
cholesterol molecules. Cholesterol reduces the area per lipid and compresses
the bilayer lateral (xy) area, resulting in a slight increase in the water
layer thickness. I have performed exactly
Well 1 nm / 3 ns is definitely not reasonable! That is about 1 m /
s ... 3.6 km/h
We has seen motion of the COM of a bilayer using CG models but the
motions
were ~ 0.1 nm on the mircosecond timescale! This is due to the way COM
is
removed ... not exact but appears only on large time
Justin, you understood it correctly; I only have problems with the low
cholesterol concentration.
According to g_traj -com the COM of DPPC in one of the simulations moves 0.6 nm
in 3.5 ns. And as Xavier just wrote it's quite much...
My mdp file looks like this:
title=
Hello,
I am not sure if anyone else has some experience with this, but I
want to simulate a hard sphere in a solvent (water and heptane). I
believe for the hard spheres, the attractive terms for LJ potential is
very negligible so the only term to take into account is repulsion,
from
Dear Justin,
Thank you for your answer. Regarding the message below:
1- How is it possible to have a reasonable max force but not a resonable
potential?
2- To remove this high potential from system, What do you suggest?
2-1 Do I need to reduce the number of molecules in the box (reduce
ERIKSSON, EMMA wrote:
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p= 1.0 1.0e-14
compressibility = 4.5e-5 4.5e-15
I would bet almost anything that this is the cause of your problem. How did you
come up with these
ERIKSSON, EMMA wrote:
I was using those strange values of tau_p and compressibility to keep the z
box length fixed in order to avoid problems associated with scaling the
positions of the molecules in the box when we constrain the distance between
DPPC and the small molecule. I was told to use
Justin A. Lemkul wrote:
ERIKSSON, EMMA wrote:
I was using those strange values of tau_p and compressibility to
keep the z
box length fixed in order to avoid problems associated with scaling the
positions of the molecules in the box when we constrain the distance
between
DPPC and the small
Hi Fabrizio,
Could you send me the input files and I'll take a look at it. You can send it
to bjelk...@cbr.su.se
Regards,
Pär Bjelkmar
29 apr 2010 kl. 16.34 skrev gmx-users-requ...@gromacs.org:
Message: 3
Date: Thu, 29 Apr 2010 10:33:53 -0400
From: Justin A. Lemkul jalem...@vt.edu
Dear experts,
Could you please take a look at energy values. The system contains only
stack of hexane molecules. MD sun gives lincs warning.
1- How can I get rid of high repulsive potential?
*genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o
Hexane-stack.gro*
Hello,
I am doing normal mode analysis for my ststem.
I run the following command.
g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg
I could genrate the eigenfreq.xvg file.
Can you tell what the units for wavenumber.
It giving the unit [cm\S-1\N].
How can I convert to cm-1?
Thanks
Nilesh
--
Nilesh Dhumal wrote:
Hello,
I am doing normal mode analysis for my ststem.
I run the following command.
g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg
I could genrate the eigenfreq.xvg file.
Can you tell what the units for wavenumber.
It giving the unit [cm\S-1\N].
How can I convert to cm-1?
Here's an excellent learning experience.
1. Simplify the problem: minimize and attempt to equilibrate one single hexane
molecule before trying to build your stacked structure. If the system blows up
here, then the topology is likely to blame. More on this in a few moments.
2. Watch the
Justin A. Lemkul wrote:
Here's an excellent learning experience.
1. Simplify the problem: minimize and attempt to equilibrate one single
hexane molecule before trying to build your stacked structure. If the
system blows up here, then the topology is likely to blame. More on
this in a
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